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1. gt Queue ai User statistics Plugins Installed plug ins CLC Genomics Algorithms version 1 7 by CLC bio Uninstall CLC Genomics Algorithms Install new plug in Install Plug in A Audit log gt External applications BETA Figure 3 2 Installing and uninstalling server plugins CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 24 Click the Browse button and locate the plug in cpa file to install a plug in To uninstall a plug in simply click the button next to the plug in The server does not need to be restarted after installation uninstallation of plug ins If you are running a job node setup you only need to install the plug in on the master server However you need to check that the plugin is enabled for each job node by going to the Job Distribution tab in the master nodes web administrative interface and clicking on the link to each job node Read more about developing server plug ins at http www clcdeveloper com 3 9 Queue Clicking the Queue panel will show a list of all the processes that are currently in the queue including the one in progress An example is shown in figure 3 3 E Queue Powerful workstation RMA Seq Saving results smoensted _ S Small workstation Ss smoensted E Medium workstation j smoensted LJ S 1 De Novo Assembly smoensted L I Z De Novo Assembly smoensted L JL 3 Reference Assembly smoensted L_ Figure 3 3 The process queue For each process
2. Bibliography Zerbino and Birney 2008 Zerbino D R and Birney E 2008 Velvet algorithms for de novo short read assembly using de Bruijn graphs Genome Res 18 5 821 829 TD Index Active directory 26 AD 26 Attributes 35 Automation 6 Back up attribute 37 Bibliography 76 BLAST 55 Command line installation 13 Cores restrict usage 22 CPU restrict usage of 22 Custom fields 35 Encrypted connection 2 External applications 58 Freezer position 35 GSSAPI 26 HTTPS 72 Kerberos 26 LDAP 26 Memory allocation 22 Meta data 35 permissions 31 Pipeline 67 Quiet installation 13 RAM 22 Recover removed attribute 37 Recycle bin 33 References 6 Scripting 6 7 Secure socket layer 2 Silent installation 13 SSL 72 System requirements 8 tmp directory how to specify 21 vmoptions memory allocation 22 Workflow 67 Xmx argument 22 ff
3. The installer also has a silent installation mode which is activated by the q parameter when running the installer from a command line e g CLCGenomicsServer_3_0 exe q CHAPTER 2 INSTALLATION 14 On Windows if you wish to have console output console can be appended as the second parameter this is only needed when running on Windows where there is no output per default CLCGenomicsServer 3 0 exe q console You can also in silent mode define a different installation directory dir CLCGenomicsServer 3 0 exe q console dir c bioinformatics clc Note Both the console and the dir options only work when the installer is run in silent mode The q and the console options work for the Uninstall program as well 2 4 Upgrading an existing installation Upgrading an existing installation is very simple For a single Genomics Server the steps we recommend are e Make sure that nobody is using the server see section 4 4 A standard procedure would be to give users advance notice that the system will be unavailable for maintenance e Install the server in the same installation directory as the one already installed All settings will be maintained If you have a CLC job node setup you will also need to upgrade the CLC Science Server software on each job node Upgrading the software itself on each node is all you need to do Configurations and plug ins for job nodes are pushed to them by the master node 2 4 1 Upgrading
4. CLC Science Server User manual Administrator Manual for CLC Science Server 2 2 Windows Mac OS X and Linux March 19 2013 This software is for research purposes only CLC bio Finlandsgade 10 12 DK 8200 Aarhus N p Denmark o LLL bio Contents 1 Introduction 1 1 System requirements 1 ee sra luge WHEW amp Paw ea hee cee Dee eee Ea Mew ea ee wee ee Installation 2 1 Quick installation guide nee aan be be Ee eR ew HEGRE a 2 2 Installing and running the Server 1 0 ee a 2 2 1 Installing the Server software n nonono we ee te amp 3 SSCS OUI og se i soe ee hee eet RR Ge eho wren ee ge RR R R 2 4 Upgrading an existing installation 0 02 eee ee ee es 2 4 1 Upgrading major versions 1 oaoa o e rr 2 5 Allowing access through your firewall 1 ee a 2 6 Downloading a license 1 a a 2 6 1 Windows license download 6 a e 6m amp Hw Sw we SA Bo oom ew a 2h Mac OS license GOWNS s i lt Xw ee nee GEE ES Ke eo Be ae ES Ss 26 3 Linux INCENSE GOwWNIOAQ s a s ache dk eR Re Dee he ee RA A E 2 Starting and stopping the server 0 6 eee ee ee 2 1 Microsoft WIndOWS fn cw Swe ew ee we ee CERA ee EM E NL E Dive MICO E eee eee ee es Se eee eee Bee eee Se Ee Coe US ERR Ree ee ea Ree ee a ee eee eee A 2 8 Installing relevant plug ins in the Workbench 058 25085 Configuring and administering the server 3 1 Logging into the administrative interface 1 we
5. Close Figure 10 1 Check system Failed elements will be marked with a red X If you have not configured your Server to submit jobs to a local Grid system or if you have and your setup is configured correctly you will see a green checkmark beside the Grid setup status item in the diagnostic report Export data C2 Import data ra Admin Submit or download bug report Submit bug report to CLC bio or download locally Thank you for taking your time to do this Your feedback is important to us Your email address Message to CLC bio Cancel Download Bug Report Submit Bug Report to CLC bio Figure 10 2 Submitting a bug report to CLC bio lf the server does not have access to the internet you can Download bug report This will create a zip file containing all the information and you can pass that on to CLC bio support If the server has access to the internet you can Submit Bug Report to CLC bio Note that the process of gathering the information for the bug report can take a while especially for job node set ups If a Workbench user experiences a server related error it is also possible to submit a bug report from the Workbench error dialog This report will include the same archive as when submitting a bug report from the web interface All data sent to support clcbio com is treated confidentially CHAPTER 10 APPENDIX 2 No password information is included in the bug report 10 2 Database configura
6. The parallel environment selected by its name must be setup by the grid administrator documentation provided by Oracle will cover this subject area in such a way that the number of slots corresponds to the number of cores SMIN CORE and S MAX CORE specify a range of cores which the jobs submitted through this grid preset can run under Care must be taken not to set SMIN CORE too high as the job might never be run e g if there is no system with that many cores available and the submitting user will not be warned by this fact An example of a native specification using parallel environments is the following cfl 1 gqname 32bit pe cle ds Here the clc parallel environment is selected and 1 to 3 cores are requested Older versions of the CLC Genomics Server CLC Genomics Server version 4 0 and older utilize CPU cores equal to the number of allocated Slots unless a parallel environment is in use in which case the behaviour is the same as described previously In many situations the number of allocated slots is 1 effectively resulting in CLC jobs running on one core only Configuration of PBS Pro With PBS Pro it is not possible to specify a range of cores at least not to our knowledge Here one specifies exactly how many cores are needed This request can be granted the process is scheduled or denied the process is not scheduled It is thus very important to choose a realistic number The number of cores are requested as a res
7. ca TOUDESROOUNE otk eee eee Eee eee eee LESSA TAS E 8 7 7 1 Checking the configuration 2242245246508 8254584546 6 8 7 2 Check your third party application aoao oaoa a a a 8 7 3 Is your Import Export directory configured 0 4 SA Gheck your NAMNE s ra saasaa a a RAS TESE 9 Workflows 9 1 Installing and configuring workflows a nonoa a a 9 2 Executing WOIKNIOWS s oaoa a a EM ER He O EGS 10 Appendix TOL MONDE ou o s eaaa a a a READE GEE DE bE DRED GEE E a 10 1 1 Check Set UD o or esre ee SAS Os ow AD d 10 1 2 BUG reDOrUNE 2k sa saaa ee a oei aa RRR RE he Be Se a 10 2 Database configurations 0404046 2 oa o a ES E E ee a ee E 10 2 1 Configurations for MYSQL aaoo dd eee ew Sw w i 10 3 SS LOC CO rsss E Bee eH E O ee ee YG 10 3 1 Enabling SSL on the server 2 3 ee ma Sds dE a ipa of 58 59 61 61 62 62 62 62 62 63 63 64 65 65 65 66 66 66 67 67 67 CONTENTS Creating a PKCS12 keystore file 0 2 eeu eee 10 3 2 Logging in using SSL from the Workbench 10 3 3 Enabling redirection from non ssl port to ssl enabled port 10 3 4 Logging in using SSL from the CLC Server Command Line Tools Bibliography Index 3 3 3 14 76 76 Chapter 1 Introduction The CLC Server is the central part of CLC bio s enterprise solutions You can see an overview of the server solution in figure 1 1 For documentation on the customization and integration please see the
8. system 6 2 6 Configure grid presets The details of the communication between the master server and the grid when submitting a job is configured using grid presets The users selects a preset when starting the job as explained in section 6 2 10 To configure the presets log into the web interface of the CLC Science Server on your master machine and navigate through these tabs in the web administrative interface Admin 7 Job distribution 5 Choose the Grid Presets section and click the Create New Preset button Edit preset Submit to medium queue Preset name Submit to medium queue Native library path path to native DRMAALib libdrmaa so Shared work directory path to sharedWorkArea Path to CLC Grid Worker path to deployed clcgridworker Job category Native specification f x q medium Submit test job Cancel Save Configuration Figure 6 6 Configuring presets For each preset the following information can be set Preset name The name of the preset as it will be presented in the Workbench when starting a job see section 6 2 10 and as you will be able to refer to it when using the Command Line Tools Alphanumeric characters can be used and hyphens are fine within but not at the start of preset names Native library path The full path to the grid specific DRMAA library Shared work directory The path to a directory that can be accessed by both the CLC Server and the Grid Workers Temporary directories
9. 2 File Manage Users and Groups This will display the dialog shown in figure 4 5 q Group management es Users Membership Groups test readonly test user db Add Figure 4 5 Managing users 4 3 1 Managing users through the Workbench Click the Add button to create a new user Enter the name of the user and enter a password You will be asked to re type the password If you wish to change the password at a later time select the user in the list and click Change password 8 To delete a user select the user in the list and click Delete 4 3 2 Managing groups through the Workbench Access rights are granted to groups not users so a user has to be a member of one or more groups to get access to the data location Here you can see how to add and remove groups and next you will see how to add users to a group Adding and removing groups is done in the Groups tab see figure 4 6 To create a new group click the Add button and enter the name of the group To delete a group select the group in the list and click the Delete button CHAPTER 4 MANAGING USERS AND GROUPS 29 S Group management Em Users Membership Groups All Groups admin everybody LabABCgroup Figure 4 6 Managing groups 4 3 3 Adding users to a group When a new group is created it is empty To assign users to a group click the Membership tab In the Selected group box you can choose amon
10. Family acc PF03143 a gt ES E Ob Gl Figure 5 9 Adding values to the attributes you will be able to search for it See below Note that the sequence needs to be saved in the data location before you can edit the attribute values When nobody has entered information the attribute will have a Not set written in red next to the attribute see figure 5 10 lann Dal CaCa T Eua Research_project Clear Cancer project Not set Figure 5 10 An attribute which has not been set This is particularly useful for attribute types like checkboxes and lists where you cannot tell from the displayed value if it has been set or not Note that when an attribute has not been set you cannot search for it even if it looks like it has a value In figure 5 10 you will not be able to find this sequence if you search for research projects with the value Cancer project because it has not been set To set it simply click in the list and you will see the red Not set disappear If you wish to reset the information that has been entered for an attribute press Clear written in blue next to the attribute This will return it to the Not set state The Folder editor provides a quick way of changing the attributes of many elements in one go see the Workbench manuals at http clcsupport com CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 39 5 4 1 What happens when the sequence is copied to another data location The user
11. Server using i either a custom GUI or the auto Workbench g CLC Genomics Server generated GUI to specify data Data Object and parameters N Data Export L Flat Input File Execution delgation B L l i The CLC Server Export Data from i the Server Data Persistence to l a flat file on the server side The format of the file is according to the setup of the integration and making use of CLC Export Frame l work i In the thin client 1 The CLC Server starts the execution of the given External Application with the given data Flat File and the given para meters l l l l l l l l l l l l l I l l l l The result of the Application i Execution is either a Flat file in a i given format OR output in std out l l l I i l l l l Flat Result File OR std out Data Import When the External Application terminates the result is imported into the Server Persistence using H the CLC Import Framework g CLC Genomics Server Data Object Post Processing When the result is imported possibly as a raw text object some post processing can be Workbench done If for example the result is a list of annotations these can be applied to the original data for example sequence CLC Genomics Server Data Object Figure 8 1 An overvie
12. This time a list of import data formats is available used to import the data back into the folder that the user selected as save destination 8 7 Troubleshooting 8 7 1 Checking the configuration Since there is no check of consistency of the configuration when it has been set up errors will only be seen on runtime when the application is executed In order to help trouble shooting in CHAPTER 8 EXTERNAL APPLICATIONS 66 case of problems there are a few things that can be done First in the error dialog that will be presented in the workbench you can see the actual command line call in the Advanced tab at the bottom This can be a great help identifying syntax errors in the call Second if you choose to import standard out and standard error as text this will make it possible to check error messages posted by the external application See figure 8 7 Y Stream handling Standard out handling Plain Text txt text Standard error handling Anything on standard error is shown as user error dialog and execution is stopped Do not stop execution or show error dialogs Plain Text LRU text Figure 8 7 Importing the result of standard error and standard out Once the set up is running and stable you can deselect these options 8 1 2 Check your third party application e Is your third party application being found Perhaps try giving the full path to it e If you are using someone else s configuration file make sure th
13. and have saved them those presets are deployed to the location you specify in the Path to CLC GridWorker field of the preset Along with the clcgridworker script the license settings file is also deployed If you need to change your license settings we recommend that you edit the license properties file under gridres settings license properties of your CLC Science Server installation and then re save each of your grid presets This will re deploy the CLC Grid Workers including the changed license properties file CHAPTER 6 JOB DISTRIBUTION 48 6 2 5 Configuring licenses as a consumable resource Since there is a limitation on the number of licenses available it is important that the local grid system is configured so that the number of CLC Grid Worker scripts launched is never higher than the maximum number of licenses installed If the number of CLC Grid Worker scripts launched exceeds the number of licenses available jobs unable to find a license will fail when they are executed Some grid systems support the concept of a consumable resource Using this you can set the number of CLC grid licenses available This will restrict the number of CLC jobs launched to run on the grid at any one time to this number Any job that is submitted while all licenses are already in use should sit in the queue until a license becomes available We highly recommend that CLC grid licenses are configured as a consumable resource on the local grid submission
14. are created within this area during each job run CHAPTER 6 JOB DISTRIBUTION 49 These temporary directories hold files used for communication between the CLC Server and Grid Worker Path to CLC Grid Worker This field should contain the path to a directory on a shared file system that is readable from all execution hosts The CLC Grid Worker along with associated settings files is extracted from the installation area of the CLC Science Server software and is then deployed to this location when you save your grid preset or whenever you update plugins on your system If this directory does not exist it will be created In versions of the Genomics Server earlier than 5 0 this path needed to point at the clcgridworker script itself To Support backwards compatibility with existing setups we ask that you do not use the name clcgridworker for a directory you wish your CLC Grid Worker to be deployed to Job category The name of the job category a parameter passed to the underlying grid system Native specification List of native parameters to pass to the grid e g associations to specific grid queues or memory requirements see below Clicking on the f x next to Native Specification pops up a box allowing the insertion of particular variables into the Native Specification box This is described further below 6 2 6 Below are examples of OGE specific arguments one might provide in the native specification field of a Grid Preset Plea
15. between the master and job node The Default temp dir setting will not work for any setup where the CLC Grid Worker will be used to submit jobs to a local grid If you work on a single server then the Shared temp dir setting can be used to specify a non default area for temporary files If you work on a master execution node setup whether it be grid nodes or CLC execution nodes the Shared temp dir must be chosen and this area must e Be configured in the Import Export directories area under the Main Configuration tab e Be a shared directory accessible to your master server and all execution nodes 8 4 3 Execute as master process The checkbox to Execute as master process can be checked if the process does not involve intensive processing on the server side Setting this means that the process will always be run on the Master server For a single server setup this has no effect However in a system with execution nodes checking this option results in the queue being effectively by passed as the job will be run directly on the master server This choice will usually only make sense for tasks that require little RAM or cpu Jobs run this way should will not actually block the queue they just run as a master process 8 5 External applications integration Parameter flow To aid in determining how the various parameters configured flow through the External Applications process you can access small graphs showing how the parameters enter
16. by clicking the blue links 2 1 2 MacOS X On Mac OS X the server can be started and stopped from the command line Open a terminal and navigate to the CLC Server installation directory Once there the server can be controlled with the following commands To start the server run the command sudo CLCScienceServer start To stop the server run the command sudo CLCScienceServer stop To view the current status of the server run the command sudo CLCScienceServer status You will need to set this up as a service if you wish it to be run that way Please refer to your operating system documentation if you are not sure how to do this 2 1 3 Linux You can start and stop the Genomics Server from the command line You can also run it as a service Command Line Open a terminal and navigate to the CLC Server installation directory Once there the server can be controlled with the following commands To start the server run the command CLCScienceServer start To stop the server run the command CLCScienceServer stop To view the current status of the server run the command CLCScienceServer status You can run these commands as any user either directly on the command or by prefacing the CHAPTER 2 INSTALLATION 18 commands with sudo e g sudo u lt username gt CLCScienceServer status Please note To run the Genomics Server as a non root user you should first ensure that the files under your CLC Science Server
17. command and within curly brackets include any parameter that needs to be configured by the user The names of the parameters inside the curly brackets will become the labels of the choices offered to the end user when they start up this external application via their Workbench In the right hand side of figure 8 2 we show how this looks if we give the co command two parameters infile and outfile External applications command name Enter name of new External applications command command line argument End user parameters for command line substitution and post processing End user parameters for command line substitution and post processing infile User selected input data v Do not export Cancel Save Figure 8 2 Setting up the co command as an external application Two drop down menus have now appeared in the blue shaded area of the right hand window in 8 2 These are dynamically generated Each parameter you enter in curly brackets in the command text box area will have a drop down menu created for it The text you entered within the curly brackets is used to label the entries in the administrative interface and are also the labels used in the end user interface presented via the Workbench The administrator now chooses the type of data each parameter will refer to The options are e Text the users is presented with a text box allowing them to enter a parameter value The administrator can provide a default value if desir
18. confirmed search Is confirmed Patent number search Patent mumber Proc LIMS number search LIMS number Idl Lab instructions search Lab instructions Figure 5 12 The attributes from figure 5 8 are now available in the Quick Search as well Read more about search in the CLC Genomics Workbench manual http www clcbio com files usermanuals CLC Genomics Workbench User Manual pdf section Lo cal search Chapter 6 Job Distribution The CLC Science Server has the concept of distributing jobs to nodes This means that you can have a master server with the primary purpose of handling user access serving data to users and starting jobs and you have a number of nodes that will execute these jobs Two main models of this setup are available a master server that submits tasks to dedicated execution nodes and a master server that submits tasks to a local grid system Figure 6 1 shows a schematic overview of these possibilities and they are described in text below CLC Genomics g Workbench a Figure 6 1 An overview of the job distribution possibilities e Model Master server with execution nodes here a master server submits CLC jobs directly to machines running the CLC Science Server for execution In this setup a group of machines from two upwards have the CLC Science Server software installed on them The system administrator assigns one of them as the master node This node controls the distribution
19. ee ee ee 3 2 Adding locations for saving data a a es 11 11 11 12 13 14 14 15 15 15 15 16 16 16 1 7 1 7 18 CONTENTS 3 2 1 Adding a file system location 0 0 eee ee ee Important points about the CLC Server data in the file system locations File locations for job node set upS 000 eee ee ee ee a 5 2 2 PO UNI thE INGE 6 sa e ed aah ae ee hee ee a ee ER ES 3 3 Changing the listening pot as Gu kha Rhea ee a ew ES SS 3 4 Changing the tmp directory 64004444 oS eee eA Oe ee we ew ee a 3 4 1 Job node setupS dS oO OSE EERE a 3 5 Setting the amount of memory available for the JVM 3 6 Limiting the number of cpus available for use n 2005 out DM COMUM a es ae E RE NE R ee EEE E ee da ee Sete MUF S UNET 2 ake eee eee eee eRe eRe eee eee EE ee 3 2 AVOR COUINES ssa eee a ve ee ee ew DEE E RE S 3 7 3 Deployment of server information to CLC Workbenches Se Ao MES qdo Di PD RE a ce ce ce R R R CO ce a a ae a are O UM 4 hee eee Eee eee eee eee ee Hoe ee 4 Managing users and groups 4 1 Logging in the first time root password 1 2 eee es 4 2 User authentication using the web interface 2 550828 ae 4 2 1 Managing users using the web interface 5008 4 2 2 Managing groups using the web interface 1 onono a a a 4 3 User authentication using the Workbench 1 a 2 eae 4 3 1 Managing users through the Workbench
20. major versions Once you have performed the steps mentioned above there are a few extra details whenever the release is more than a bug fix upgrade e g a bug fix release would be going from version 1 0 to 1 0 1 First make sure all client users are aware that they must upgrade their Workbench and server connection plug in Second check that all plug ins installed on the CLC Science Server are up to date see section 3 8 You can download updated versions of plug ins from http www clcbio com Cie plugany Third if you are using the CLC Server Command Line Tools it might have to be updated as well This is noted in the latest improvements page of the server http www clcbio com improvements genomics server Finally if you are using job nodes be aware that any new tools included in the server upgrade are automatically disabled on all job nodes This is done in order to avoid interfering with a job node set up where certain job nodes are dedicated to specific types of jobs Read more about enabling the jobs in section 6 1 3 For major versions e g going from 1 X to 2 0 a new license needs to be downloaded see section 2 6 and the server restarted CHAPTER 2 INSTALLATION 15 2 5 Allowing access through your firewall By default the server listens for TCP connections on port 7777 See section 3 3 for info about changing this If you are running a firewall on your server system you will have to allow incoming TCP co
21. means that depending on how you have configured your system the job that is number one in the queue will not necessarily be processed first After your job nodes are all configured file system locations should be added see the section on Adding a file system location 3 2 1 We recommend this is done at this point as all job nodes will then inherit the configurations made on the master node In order to test that access works for both job nodes and the master node you can perform the following check 1 Create a new folder in the Workbench in the new data location on disk this will be done by the master node Import some data into this folder 2 In the Workbench run one of the analyses in the server toolbox and choose to save the results in the new folder this will be done by the job node 3 Once finished try to rename one of the result files in the Workbench on disk this will be done by the master node If this works it means that both master and job nodes are able to write to the same files One relatively common problem that can arise here is root squashing This often needs to be disabled because it prevents the servers from writing and accessing the files as the same user read more about this at http nfs sourceforge net faq_bll 6 1 4 Installing Server plug ins Server plugin installation is described in section 2 2 You only need to install the plug in on the master server Once installed you should check that
22. of jobs The other nodes are execution nodes which carry out the computational tasks they are assigned The execution nodes wait for the master node to assign them a job and once the job is executed they are available for the next job With this set up the CLC master server controls the queue and the distribution of compute resources This has the advantage of being simple to set up and maintain with no other software required However It is not well suited to situations where the compute resources are shared with other systems because there is no mechanism for managing the load on the computer This setup works best when the execute nodes are machines dedicated to running a CLC Science Server Further details about this setup can be found in section 6 1 e Model Il Master server submitting to grid nodes here the master server submits jobs to a third party job scheduler That scheduler controls the resources on a local computer 40 CHAPTER 6 JOB DISTRIBUTION 41 cluster grid where the job will be executed This means that it is the responsibility of the native grid job scheduling system to start the job When the job is started on one of the grid nodes a CLC Grid Worker which is a stand alone executable including all the algorithms on the server is started with a set of parameters specified by the user Further details about this setup can be found in section 6 2 6 1 Model Master server with execution nodes The general steps to
23. the command expression is created in this case opt local velvet clcbio velvet sh hash size read type reads expected coverage contigs The first is the path to the script and the following are parameters that are interpreted by the server when calling the script because they are surrounded by curly brackets Note that each parameter entered in curly brackets gets an entry in the panel below the command line expression The first one hash size can be entered as a Double which is a number in computer parlance and it is thus up to the user to provide a value A default value is entered here in the configuration 31 The second one is the read type which has been configured as a CSV enum which is basically a list The first part consists of the parameters to be used when calling the script short shortPaired long longPaired andthe second part is the more human readable representation that is shown in the Workbench Short Short Paired Long Long Paired The third parameter is reads which is the input data When the User selected input data option is chosen a list of all the available export formats is presented In this case Velvet expects a fasta file When a user starts Velvet from the Workbench the server starts exporting the selected input data to a temporary fasta file before running the script The expected coverage Is similar to hash size The last parameter is contigs which represents the output file
24. which only schedules a single job on any given machine at a time Otherwise your CLC jobs may conflict with others running on the same execution host at the same time Configuration of OGE SGE 1 CPU Core usage when not using parallel environment By default the CLC Genomics Servers ignores the number of slots assigned to a grid job and utilizes all cores of the execution host That is jobs will run on all cores of a execution host As of version 4 01 of the CLC Genomics Server there is an environmental variable which when set to 1 will specify that the number of allocated slots should be interpreted as the maximum number of cores a job should be run on To set this environmental variable add the following to the native specification of the grid preset y CLC USE OGE SLOTS AS CORESI In this case the number of utilized cores is equal to the number of slots allocated by OGE for the job 2 Limiting CPU core usage by utilizing parallel environment CHAPTER 6 JOB DISTRIBUTION 51 The parallel environment feature can be used to limit the number of cores used by the CLC Genomics Server when running jobs on the grid The syntax in the native specification for using parallel environments is pe SPE NAME SMIN CORE SMAX CORE When the parallel environments feature is used the number of allocated slots is interpreted as the number of cores to be used That is the number of utilized cores is equal to the number of slots in this case
25. you are able to Cancel and re prioritize the order of the processes by clicking the up and down arrows Some processes also allow you to pause and resume At the top you can see the progress of the process that is currently running If you are running a CLC Server with execution nodes you can also Stop and requeue 1 a job that is currently being processed Chapter 4 Managing users and groups 4 1 Logging in the first time root password When the server is installed you will be able to log in via the web interface using the following credentials e User name root e Password default Once logged in you should as a minimum set up user authentication see section 4 2 and data locations see section 3 2 before you can start using the server For security reasons you should change the root password see figure 4 1 Admin Authentication Change root password Note that if you are going to use job nodes it makes sense to set these up before changing the authentication mechanism and root password see section 6 Element Info CD History Sequence Text Download C3 Upload Main configuration Authentication Y change root password Current password eese New password 6666666 Verify password eeeee sel J Change Root Password P Authentication mechanism Figure 4 1 We recommend changing the root password The verification of the root password is shown with the green checkm
26. your operating system you may be prompted for your password as shown in figure 2 1 or asked to allow the installation to be performed e On Windows 7 or Vista you will need to right click on the installer file icon and choose to Run as administrator e For the Linux based installation script you would normally wish to install to a central location which will involve running the installation script as an administrative user either by logging in as one or by prefacing the command with sudo Please check that the installation script has executable permissions before trying to execute it ANOO Enter Password Please enter your password You must be a member of the Administrator group OK L Cancel Figure 2 1 Enter your password Next you will be asked where to install the server 2 2 If you do not have a particular reason to change this simply leave it at the default setting The chosen directory will be referred to as the server installation directory throughout the rest of this manual The installer allows you to specify the maximum amount of memory the CLC Server will be able to utilize 2 3 The range of choice depends on the amount of memory installed on your system and on the type of machine used On 32 bit machines you will not be able to utilize more than 2 GB of memory on 64 bit machines there is no such limit If you do not have a reason to change this value you should simply leave it at the default setting If y
27. 011 05 25 35640 DNA assemblies alt_CRA_TCAGchr7v2_contig alt CRA TCAGchr v2_contig 2011 10 07 6 DNA alt HuRef contig alt HuRef contig 2011 10 07 4530 DNA alt contig Mus musculus build 37 genome database alternate 2010 11 09 13033 DNA assembly Mm Celera only Figure 7 3 Selecting database to BLAST against 7 2 Adding and removing BLAST databases Databases can be added in two ways e Place pre formatted databases in the directory selected as BLAST database location on the server file system The CLC Science Server will automatically detect the database files and list the database as target when running BLAST You can download pre formatted database from e g ftp ftp ncbi nih gov blast db e Run the Create BLAST Database 24 tool via your Workbench and choose to run the function on the Server when offered the option in the Workbench Wizard You will get a list of the BLAST database locations that are configured on your Server The final window of the wizard offers you a location to save the output to The output referred to is the log file for the BLAST database creation The BLAST databases themselves are stored in the designated BLAST database folder you chose earlier in the setup process A note on permissions To create BLAST databases on the Server using the Workbench interface the user running the CLC Genomics Server process must have file system level write permission on the import export directory that you have configu
28. 052 25885 4 3 2 Managing groups through the Workbench aoao oaoa a a a 4 3 3 Adding users toa group 2 oa a a 4 4 User statistics 0 00 eee ee ee ee ke kk kk ee 5 Access privileges and permissions 5 1 Controlling access to data 2 64 eis tee ree bee ewe a 5 1 1 Setting permissions onafolder 0 000 a Permissions on the recycle bin 1 a ee 5 1 2 Technical notes about permissions and security 5 2 Global permissions lt 2 i 46 bbs eae d bie Ge beeen es bbe ee hE es CONTENTS 5 3 Customized attributes on data locations 5 3 1 Configuring which fields should be available 5 9 2 EQUMBIRIO 2224 he gee bo mms 5 3 3 Removing attributes 5 3 4 Changing the order of the attributes 5 4 Filling in values 00 4 5 4 1 What happens when the sequence is copied to another data location Gita SOMME uniram RR awiu 6 Job Distribution 6 1 Model Master server with execution nodes 6 1 1 Master and job nodes explained 6 1 2 User credentials on a master job node setup 004 6 1 3 Configuring yoursetup 6 1 4 Installing Server plug ins 6 2 Model Il Master server submitting to grid nodes 6 2 1 Requirements for CLC Grid Integration 6 2 2 Technical overview 6462626424 3 6 2 3 Setting up the grid integration 6 2 4 Licensing of grid workers 6 2 5 Configuring licenses as a consumable res
29. 5 4 Setting permissions for an alorithm The default configuration is that all users have access to everything CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 35 5 3 Customized attributes on data locations The CLC Science Server makes it possible to define location specific attributes on all elements stored in a data location This could be company specific information such as LIMS id freezer position etc Note that the attributes scheme belongs to a location so if you have added multiple locations they will have their own separate set of attributes 5 3 1 Configuring which fields should be available To configure which fields that should be available right click the data location Location Attribute Manager This will display the dialog shown in figure 5 5 g Manage attributes Attribute info No attributes are selected db Add Attribute Figure 5 5 Adding attributes Click the Add Attribute gt button to create a new attribute This will display the dialog shown in figure 5 6 Create Attribute General attribute info Bounded decimal number Figure 5 6 The list of attribute types First select what kind of attribute you wish to create This affects the type of information that can be entered by the end users and it also affects the way the data can be searched The following types are available lf the data location is a server location you need to be a server administrator to do this CHAP
30. OMMAND_NAME The name of the CLC Science Server command to be executed on the grid by the clcgridworker executable COMMAND ID The ID of the CLC Science Server command to be executed on the grid These variables can be added by the administrator directly into the Native Specification box by surrounding the variable name with curly brackets Alternatively to ensure the proper syntax you can click on the f x link and choose the variable to insert These variables can be used by the administrator in any way that fits with the native grid system and that does not cause clashes with the way the CLC Server and Grid Workers communicate For example in cases where grid usage is closely monitored it may be desirable to include the user name of the analysis job in metadata reports so that computer resource time can be logged Another example might be to set an option such as q COMMAND_NAME if there were for example certain commands to be submitted to queues of the same name as the commands 6 2 7 Controlling the number of cores utilized In order to configure core usage the native specification of the grid preset needs to be properly configured This configuration depends on the grid system used From version 4 01 of the CLC Genomics Server all cores on an execution node will be used by default Unless otherwise configured to limit the number of cores used for a job involving assembly or read mapping phases a dedicated queue must then be setup
31. TER 5 ACCESS PRIVILEGES AND PERMISSIONS 36 e Checkbox This is used for attributes that are binary e g true false checked unchecked and yes no e Text For simple text with no constraints on what can be entered e List Lets you define a list of items that can be selected explained in further detail below e Number Any positive or negative integer e Bounded number Same as number but you can define the minimum and maximum values that should be accepted If you designate some kind of ID to your sequences you can use the bounded number to define that it should be at least 1 and max 99999 if that is the range of your IDs e Decimal number Same as number but it will also accept decimal numbers e Bounded decimal number Same as bounded number but it will also accept decimal numbers e Hyper Link This can be used if the attribute is a reference to a web page A value of this type will appear to the end user as a hyper link that can be clicked Note that this attribute can only contain one hyper link If you need more you will have to create additional attributes When you click OK the attribute will appear in the list to the left Clicking the attribute will allow you to see information on its type in the panel to the right 5 3 2 Editing lists Lists are a little special since you have to define the items in the list When you click a list in the left side of the dialog you can define the items of the list in the panel to t
32. ading an existing license file this needs to be deleted from the licenses folder When you run the downloadlicense script it will create a new license file Restart the server for the new license to take effect Restarting the server is covered in in section 2 7 3 2 1 Starting and stopping the server 2 7 1 Microsoft Windows On Windows based systems the CLC Science Server can be controlled through the Services control panel Choose the service called CLCScienceServer and click the start stop or restart link as shown in figure 2 6 CHAPTER 2 INSTALLATION Lr H Services File Action view Help E EB a Services Local Services Local CLCServer Name Description Status Ra Background Intelligent Transfer Service Transfers files in the background Stop the service a Bluetooth Support Service Started Ra Brsplservice Restart the service CLCServer CLC Genomics Server Started cpa cine S Sa ClipBook Enables ClipBook Viewer to store Ra COM Event System Supports System Event Notificati Started Sa COM System Application Manages the configuration and tr Ra Computer Browser Maintains an updated list of comp Sa Cryptographic Services Provides three management serv Started 4 DCOM Server Process Launcher Provides launch Functionality for Started SRA DHCP Client Manages network configuration b Started lt b Extended Standard Figure 2 6 Stopping and restarting the server on Windows
33. and validated it becomes available for execution When you log in on the server using the CLC Workbench workflows installed on the server automatically become 67 CHAPTER 9 WORKFLOWS 68 Simple variant detection and annotation Simple variant detection and annotation 0 1 Build 171112 2204 by Support This workflow has internal errors Report a bug Workflow Input Map Reads to Reference J Dick to change configuration Probabilistic Vari E a Reads Track Predict Spice Site Effect Gick fo change configuration Amino Azid Changes J Gick to change coOnfmiguretion Anmotatad Variant Track Save Workflow Test Workflow Figure 9 1 A workflow is installed and validates available in the Toolbox see figure 9 3 When you select it you will be presented with a dialog as shown in figure 9 4 with the options of where to run the workflow This means that workflows installed on the server can be executed either on the server or in the workbench In the same way workflows installed on the workbench can be executed on the server as well as on the workbench The only requirement is that both the tools that are part of the workflow and any reference data are available An important benefit of installing workflows in the server is that it provides the administrator an easy way to update and deploy new versions of the workflow because any changes immediately take effect for all workbench
34. ark 4 2 User authentication using the web interface When the server is installed you can log in using the default root password username root password default Note that if you are going to use job nodes it makes sense to set this up first before changing the authentication mechanism and root password see section 6 25 CHAPTER 4 MANAGING USERS AND GROUPS 26 Once logged in you can specify how the general user authentication should be done Admin 173 Authentication Authentication mechanism This will reveal the three different modes of authentication as shown in figure 4 2 3f Element Info CD History Sequence Text 4 Download 4 Upload 5 Main configuration Authentication P change root password Y authentication mechanism Built in authentication O pap directory O active directory save Configuration 5 Job nodes gt Queue User statistics lt Plugins Audit log Figure 4 2 Three modes of user authentication The options are e Built in authentication This option will enable you to set up user authentication using the server s built in user management system This means that you create users set passwords assign users to groups and manage groups using the web interface see section 4 2 1 or using the Workbench see section 4 3 1 All the user information is stored on the server and is not accessible from other systems e LDAP directory This option will allow you to use an
35. at are performed on the system as shown in figure 10 1 If any of the tests fail it will be shown in the list You can expand each of the tests to display more information about what the test is checking and information about the error if it fails 10 1 2 Bug reporting When contacting support clcbio com regarding problems on the server you will often be asked for additional information about the server set up etc In this case you can easily send the necessary information by submitting a bug report Log in to the web interface of the server as administrator report a bug at the top right corner Enter relevant information with as much detail as possible Submit Bug Report to CLC bio You can see the bug report dialog in 10 2 The bug report includes the following information e Log files e A subset of the audit log showing the last events that happened on the server e Configuration files of the server configuration In a job node set up you can include all this information from the job nodes as well by checking the Include comprehensive job node info checkbox in the Advanced part of the dialog 10 CHAPTER 10 APPENDIX 11 r setup diagnostics Generate diagnostics report ff Master and job nodes version match sf Job distribution J File system locations consistency ff Job nodes configuration integrity J K Job nodes plugin integrity ff Index server status ff File system locations permissions Grid setup status
36. ata using for example general system tools the permissions set on the data in CLC Science Server has no effect CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 34 5 2 Global permissions In the server web interface in the Admin tab you can set global permissions for the CLC Science Server as shown in figure 5 3 f Element Info CD History Sequence Text Export data Hi Import data 3 Main configuration Authentication Global permissions gt Algorithms External applications core tasks gt Import export directories CE Job distribution Figure 5 3 Global permissions Permissions can be set for Algorithms All the algorithms running on the server are listed here External applications All the external applications configurations are listed here Core tasks These are general import export and maintenance tasks import export directories Permissions can be set for each of the directories defined You can specify which groups should have access by clicking the Edit Permissions button A dialog will appear like that in figure 5 4 If you choose Only authorized users from selected groups you will be offered a list of groups that you can select or de select to give or take away access to that functionality ermissions for Annotate and Merge Counts Listing and execution of Annotate and Merge Counts is granted to 9 All authorized users Only authorized users from selected groups Figure
37. ation directory this is the script tying the two Velvet program together You need to edit the script if you did not place the Velvet binary files in usr local velvet e Make sure execute permissions are set on the script and the executable files in the Velvet installation directory Note that the user executing the files will be the user who started the Server process if you are using the default start up script this will be root e Use the velvet xm1 file as a new configuration on the server Log in to the server via the web interface and go to the External applications tab under Admin Gra and click Import Configuration When the configuration has been imported click the CLC bio Velvet header and you should see a configuration as shown in figure 8 5 Update the path to the Velvet installation at the very top if necessary CHAPTER 8 EXTERNAL APPLICATIONS 64 T CLC bio Velvet External applications command name CLC bio Velvet command line argument opt local velvet clcbio velvet sh hash size read type reads expected coverage contigs End user parameters for command line substitution and post processing hash size Double v 31 read type CSV enum vy short shortPaired lon Short Short Paired Lon reads User selected inputdata FASTA fa fsa fasta v expected coverage Double v 10 contigs Output file from CL v FASTA fa fsa fasta v contigs Figure 8 5 The Velvet configuration has been imp
38. be able to read from or write to it 5 1 1 Setting permissions on a folder This step is done from within a CLC Workbench Start up a copy of a Workbench that has the CLC Workbench Client plugin installed From within the Workbench go to the File menu and choose the item CLC Server Login Log into the CLC Server as an administrative user You can then set permissions on folders in your database if you have one or on folders within file system locations that have had permissions enabled right click the folder 71 Permissions This will open the dialog shown in figure 5 2 Set the relevant permissions for each of the groups and click OK If you wish to apply the permissions recursively that is to all subfolders check Apply to all subfolders in the dialog shown in figure 5 2 Note that this operation is only relevant if you wish CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 33 Le Permissions Read permission Write permission Apply to all subfolders Ke Figure 5 2 Setting permissions on a folder to clean up the permission structure of the subfolders It should be applied with caution since it can potentially destroy valuable permission settings in the subfolder structure Permissions on the recycle bin The recycle bin is conceptually a folder like any else It is special in the sense that all users must have write access otherwise they will not be able to delete anything Because there is one recycle bin for the data
39. ble to the full path of your java binary Then re save each of your grid presets so that this altered clegridworker script is deployed to the location specified in the Path to CLC GridWorker field of your preset e Is the SGE ROOT variable set early enough in your system that it is included in the environment of services Alternatively did you edit the Genomics Server startup script to set this variable If so the script is overwritten on upgrade you will need to re add this variable setting either to the startup script or system wide in such a way that it is available in the environment of your services CHAPTER 6 JOB DISTRIBUTION 54 e Is your java 64 bit while your DRMAA library is 32 bit or vice versa These two things must be either both for 64 bit systems or both for 32 bit systems 6 2 12 Understanding memory settings Most work done by the CLC Genomics Server is done via its java process However particular tools involving de novo assembly or mapping phases e g read mappings RNA seq analyses smallRNA analyses etc use C binaries for the computational phases Java process For the grid worker java process if there is a memory limit set in your clegridworker vmoptions file this is the value that will be used See section 6 2 8 If there is no memory setting in your grid worker s clegridworker vmoptions file then the following sources are referred to in the order stated As soon as a valid setting is found that is t
40. by selecting an attribute and click the Up and Down arrows in the dialog This will affect the way the attributes are presented for the user as described below 5 4 Filling in values When a set of attributes has been created as shown in figure 5 8 the end users can start filling in information g Manage attributes Attribute info Type List Hyperlink Name Research_project Is_confirmed Cancer project Stem cell project db Add Attribute Remove Attribute 7 Fe Figure 5 8 A set of attributes defined in the attribute manager This is done in the element info view right click a sequence or another element in the Navigation Area Show 42 Element info 5 This will open a view similar to the one shown in figure 5 9 You can now enter the appropriate information and Save When you have saved the information CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 38 IW AR Latin name Edit Homo sapiens Common name Edit human Taxonomy name Edit Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Eutheria Euarchontoglires Primates Haplorrhini Catarrhini Hominidae Homo m EE ian E De pa Lari lda Research project Clear Cancer project L Patent number Clear 11 782 Is confirmed Clear 7 LIMS number Clear E 204 mM Location Clear Lab 23 Lab instructions Edit Clear Hyperlink Edit Clear http pFam sanger ac uk
41. constraint gt lt display name gt Security Constraint lt display name gt lt web resource collection gt lt web resource name gt SSL restricted Area lt web resource name gt lt url pattern gt lt url pattern gt lt web resource collection gt lt user data constraznt gt lt transport guarantee gt CONFIDENTIAL lt transport guarantee gt lt user data constraint gt lt security constraint gt The above section is commented out in the supplied conf welb xml file and just has to be commented in in order for redirection to work Please note that this redirection only works for the browser accessing the web interface When connecting from the Workbench the correct port has to be specified 10 3 4 Logging in using SSL from the CLC Server Command Line Tools The CLC Server Command Line Tools will also automatically detect and use SSL if present on the port it connects to If the certificate is untrusted the clcserver program will refuse to login CHAPTER 10 APPENDIX 15 clcserver S localhost U root W defaullt P 7778 Message Trying to log onto server Error SSL Handshake failed Check certificate Option Description A lt Command gt Command to run If not specified the list of commands on the server will be returned C lt Integer gt Specify column width of help output D lt Boolean gt Enable debug mode default false G lt Grid Preset value gt Speci
42. developer kit for the serverathttp www clcdeveloper com The CLC Science Server is shipped with the following tool that can be started from the Workbench e BLAST creation of databases and running BLAST e Find primer binding sites e Annotate secondary peaks Sanger data e External applications integrating with 3rd party programs on the server The functionality of the CLC Science Server can be extended by installation of Server plug ins The available plug ins can be found at http www clcbio com server plugins 1 1 System requirements The system requirements of CLC Science Server are e Windows XP Windows Vista or Windows 7 Windows Server 2003 or Windows Server 2008 e Mac OS X 10 6 or later However Mac OS X 10 5 8 is supported on 64 bit Intel systems e Linux Red Hat or SUSE e 32 or 64 bit e 256 MB RAM required e Minimum of 2 GB RAM recommended more may be required depending on the data and analysis to be run CHAPTER 1 INTRODUCTION 9 Clients CLC Genomics E Browser Workbench UOI EZIWO SN 4 Scalability f ea Bioinformatics Database database schemas Data backend Figure 1 1 An overview of the server solution from CLC bio Note that not all features are included with all license models 1 2 Licensing There are three kinds of licenses needed for running the CLC Science Server e A license for the server This is needed for running the server The license will allo
43. e all included in the license on the master node To configure your master execution node setup navigate through these tabs in the web admin istrative interface on your master node Admin 575 Job distribution 155 First set the server mode to MASTER_NODE and provide the master node address port and a human readable name as shown in figure 6 3 OS Job distribution Server mode MASTER NODE Managing processing v Master node host clcmaster Master node port 7777 Master node displayname CLCMaster Save Configuration Figure 6 3 Setting up a master server Next click Attach Node to specify a job node Fill in the appropriate information about the node see figure 6 4 Besides information about the node hostname port and displayname you can also configure what kind of jobs that node is able to execute Repeat this process for each job node you wish to attach and click Save Configuration when you are done Once set up the job nodes will automatically inherit all configurations made on the master node At any time you can log in to a job node itself via its Server administrative interface Note that you will get a warning dialog if there are types of jobs that are not enabled on any of the nodes Note that when a node has finished a job it will take the first job in the queue that is of a type CHAPTER 6 JOB DISTRIBUTION 43 Figure 6 4 Setting up a master server the node is configured to process This then
44. e location to the third party application is correct for your system e f you are using someone else s wrapper scripts make sure all locations referred to inside the script are correct for your system e Is your third party application executable e f there was a wrapper script being used to call the third party applciation is that wrapper script executable 8 7 3 Is your Import Export directory configured For certain setups you need to have Import Export directories configured Please refer to section 8 4 2 for more details on this 8 7 4 Check your naming If your users will only access the External Applications via the Workbench then you do not have to worry about what name you choose when setting up the configuration However if they plan to use the clcserver program from the CLC Command Line Tools to interact with your CLC Science Server then please ensure that you do not use the same name as any of the internal commands available You can get a list of these by running the clcserver command with your CLC Science Server details and using the A flag with no argument Chapter 9 Workflows The CLC Science Server supports workflows that are created with the CLC Workbenches A work flow consists of a series of tools where the output of one tool is connected as the input to another tool As an example a workflow could pass data through read mapping use the mapped reads as input for variant detection and perform some f
45. e served by the CLC License Server software For information on how to install the CLC License Server and download and install your CLC Grid Worker licenses please follow the instructions in the CLC License Server user manual which can be found at http www clcsupport com clclicenseserver current A pdf version is available at http www clcbio com files usermanuals CLC License Server User Manual por Step 2 Configuring the location of your CLC License Server for your CLC Grid Workers One license is used for each CLC Grid Worker script launched When the CLC Grid Worker starts running on a node it will attempt to get a license from the license server Once the job is complete the license will be returned Thus your CLC Grid Worker needs to know where it can contact your CLC License Server to request a license To configure this use a text editor and open the file gridres settings license properties under the installation are of your CLC Genomics Server The file will look something like this License Settings serverip host example com serverport 6200 disableborrow false autodiscover false useserver true You can leave autodiscover true to use UDP based auto discovery of the license server However for grid usage it is recommended that you set autodiscover false and use the serverip property to specify the host name or IP address of your CLC License Server After you have configured your grid presets see section 6 2 6
46. ed e CSV enum this allows the administrator to set a drop down list of parameter choices for the user For an example of this please see section 8 6 on setting up Velvet as an external application e User selected input data users will be prompted to select an input file from those they have stored on the CLC Server Output file from CL users will be prompted for a location to store a file that is created by the third party application An extra text box is also provided in the configuration so the administrator can specify a default name for the re imported file If no filename is provided by the administrator the basename of the file from the system is used e File users can select an input file from their local machine s filesystem e Boolean text This generates a checkbox in the end user interface labelled with the text you provide If the user clicks in the box the parameter is set to true an empty box means the parameter is set to false e Boolean compound this enables the creation of a checkbox where if checked the end user is presented with another option of your choice If the check box is not checked then that option will be greyed out Here the administrator can also choose if the box is to be checked or unchecked by default in the Workbench interface CHAPTER 8 EXTERNAL APPLICATIONS 61 e Double Allows the user to enter a number The administrator can choose a number this option should be set to by de
47. ed in the user parameters section will be used You can see an example for the very simple copy command used as an example above in figure 8 4 CHAPTER 8 EXTERNAL APPLICATIONS 63 V Parameter flow infile ne Exported by V Parameter flow FASTA falfsa fasta infile outfile Native application cp outfile Figure 8 4 An example of the parameter overview facility 8 6 External applications integration Velvet Velvet Zerbino and Birney 2008 is a popular de novo assembler for next generation sequencing data We have provided example scripts and configurations to set this up as an external application on CLC Science Server The velvet package includes two programs that need to be run consecutively Because the external application on the CLC Science Server is designed to call one program a script is needed to encapsulate this 8 6 1 Installing Velvet To get started you need to do the following e Install Velvet on the server computer download from http www ebi ac uk zerbino velvet Note that if you have job nodes it needs to be installed on all nodes that will be configured to run Velvet We assume that Velvet is installed in usr local velvet but you can just update the paths if it is placed elsewhere e Download the scripts and configuration files made by CLC bio from http www clcbio com external applications velvet zip e Unzip the file and place the clcbio folder and contents in the Velvet install
48. er to computer Therefore the installer investigates the amount of RAM during installation and sets the amount of memory that the JVM can use On Windows and Linux this value is stored in a property file called ServerType vmoptions e g CLCGenomicsServer vmoptions which contains a text like this Xmx8 000m The number 8000 is the amount of memory the CLC Science Server is allowed to use This file is located in the installation folder of the the CLC Science Server software By default he value is set to 5O of the available RAM on the system you have installed the software on You can manually change the number contained in the relevant line of the vmoptions file for your CLC Science Server if you wish to raise or lower the amount of RAM allocated to the Java Virtual Machine 3 6 Limiting the number of cpus available for use A number of the algorithms in the CLC Science Server will in the case of large jobs use all the cores available on your system to make the analysis as fast as possible If you wish to restrict this to a predefined number of cores this can be done with a properties file Create a text file called cpu properties and save it in the settings folder under the CLC Science Server installation directory The cpu properties file should include one line like this CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 23 maxcores 1 Restart the CLC Science Server if you create or change this file for these settings t
49. existing LDAP directory This means that all information needed during authentication and group memberships is retrieved from the LDAP directory If needed the LDAP integration can use Kerberos GSSAPI e Active directory This option will allow you to use an existing Active directory which is Microsoft s LDAP counterpart This means that all information needed during authentication and group memberships is retrieved from the Active directory For the two last options a settings panel will be revealed when the option is chosen allowing you to specify the details of the integration Note that membership of an administrative group is used to control which users can access the admin part of the web interface These users will also be able to set permissions on folders see section 5 For the built in authentication method this means adding particular users to the built in admin group For Active Directory or LDAP this means designating a group in the box labeled Admin group name and adding any users who should be administrators of the CLC Server to this group 4 2 1 Managing users using the web interface To create or remove users or change their password Admin Users and groups Manage user accounts This will display the panel shown in figure 4 3 CHAPTER 4 MANAGING USERS AND GROUPS Zi C Users and groups F Manage user accounts Add user account Username Password verify password Add User Change pas
50. external applications is configured in the CLC Science Server administrative web interface A special plug in needs to be installed in the client Workbench to give the end user access to the configured third party tools Please contact support clcbio com to get this Workbench plug in Figure 8 1 shows an overview of the actions and data flow that occur when an integrated external applications is executed via the CLC Workbench In general terms the basic work flow is 1 The user selects input data and parameters and starts the job from the Workbench 2 The server exports the input data to a temporary file 3 The server starts the command line application using the parameters specified from the user and the temporary file as input 4 When the command line application is done the server imports output data back into the CLC environment saving it in the data location on the server 5 The user is notified that the job is done and the results are available for viewing and further analysis in the Workbench Note that all files used and files created and saved are within the CLC environment Temporary files are created outside the CLC environment during the execution of a third party tool but are deleted after the process runs under normal circumstances 58 CHAPTER 8 EXTERNAL APPLICATIONS 59 Integration with External Application Server Side Description Client Side Server Side The user submits a Command EA Line job to the CLC
51. f CLC Gridworker licenses excess tasks are held in the queue until licenses are released In OGE for example the number of simultaneous CLC jobs sent for execution on the cluster can be controlled in this way by configuring a Consumable Resource CHAPTER 6 JOB DISTRIBUTION 45 An example of a system that works for submitting CLC jobs but which cannot be officially supported due to the second of the above points is PBS Torque As far as we know there is no way to limit the number of CLC jobs sent simultaneously to the cluster to match the number of CLC Gridworker licenses So with PBS Torque if you had three Gridworker licenses up to three jobs could be run simultaneously However if three jobs are already running and you launch a fourth job then this fourth job will fail because there would be no license available for it This limitation can be overcome allowing you to work with systems such as PBS Torque if you control the job submission in some other way so the license number is not exceeded One possible setup for this is if you have a one node runs one job setup You could then set up a queue where jobs are only sent to a certain number of nodes where that number matches the number of CLC Gridworker licenses you have DRMAA for PBS Pro Code for this can be downloaded from http sourceforge net projects pbspro drmaa When configuring the library one has to pass an with pbs argument which points to the prefix of the PBS i
52. fault If none is set then O is the default In the right hand side of figure 8 2 we set the parameters so that the input file to be sent to the system s copy command will be specified by the user and we tell the system to export this file from the CLC Server as a fasta file We then configure the import of output file from the copy command back into the CLC Server and specify that we are importing a fasta file When configuring standard bioinformatics third party applications you are able to choose from many Standard formats to export from and to import back into the CLC Science Server Once the configuration is complete and has been saved the external application should now appear in the list in the administrative web interface The small checkbox to the left of the external application name should be checked This means it is will be accessible to those with the Workbench plug in installed If a particular external application needs to be removed from end user access for a while this small box can just be unchecked 8 2 External applications integration Post processing This section is still being written 8 3 External applications integration Stream handling There is also a general configuration of stream handling available The stream handling shown in figure 8 3 allows you to specify where standard out and standard error for the external application should be handled Y Stream handling Standard out handling Do not impor
53. from all users you should be careful granting everybody read access to the recycle bin since they will then be able to see the data deleted by other users We recommend only granting read access to administrators Only administrators are allowed to empty the recycle bin 5 1 2 Technical notes about permissions and security All data stored in CLC Science Server file system locations are owned by the user that runs the CLC Science Server process Changing the ownership of the files using standard system tools is not recommended and will usually lead to serious problems with data indexing and hamper your work on the CLC Science Server One implication of the above ownership setup is that by default i e without permissions enabled all users logging into the CLC Science Server are able to access all data within that file system location and write data to that file system locations All files created within such a file system location are then also accessible to all users of the CLC Science Server Group permissions on file system locations is an additional layer within the CLC Science Server and is not part of your operating system s permission system This means that enabling permissions and setting access restrictions on CLC file system locations only affects users accessing data through CLC tools e g using a Workbench the CLC Command Line Tools the CLC Science Server web interface or the Server API If users have direct access to the d
54. fy to execute on grid H Display general help I lt Algorithm Command gt Get information about an algorithm 0 lt File gt Output file P lt Integer gt Server port number default 7777 Q0 lt Boolean gt Quiet mode No progress output default false S lt String gt Server hostname or IP address of the CLC Server U lt String gt Valid username for logging on to the CLC Server V Display version W lt String gt Clear text password or domain specific password token In order to trust the certificate the sslStore tool must be used sslStore S localhost U root W defaullt P 7778 The server localhost presented an untrusted certificate with the following attributes SUBJECT Common Name localhost Alternative Names N A Organizational Unit Enterprise Organization CLC Bio Locality Aarhus N State N A Country DK SSUER Common Name localhost Organizational Unit Enterprise Organization z CLC BIO Locality Aarhus N State N A Country DK FINGERPRINTS SHA 1 A5 F6 8D C4 F6 F3 CB 44 DO BA 83 E9 36 14 AE 9B 68 9B 9C F9 SHA 256 4B BS OB 04 3C 3A Al E2 D1 BF 87 10 F1 5D EA DD 9B 92 FF E3 C1 C9 9A 35 48 AF F6 98 87 9F 1D A8 Valid From Sep 1 2011 Valid To Aug 31 2012 Trust this certificate yn Once the certificate has been accepted the clcserver program is allowed to connect to the server
55. g all the groups that have been created When you select a group you will see its members in the list below see figure 4 7 To the left you see a list of all users Le Group management Users Membership Groups kel Selected Group admin mi Users Group Members clcuser test_admin test_admin test readonly test user Figure 4 Listing members of a group To add or remove users from a group click the Add E or Remove dE buttons To create new users see section 4 3 1 The same user can be a member of several groups 4 4 User statistics Clicking the User statistics panel will show a summary of the current usage of the server An example is shown in figure 4 8 You can see the number of users currently logged in and you can see the number of sessions for each user The two green dots indicate that this user is logged in twice e g through the Workbench and through the web interface The other two users have been logged in previously CHAPTER 4 MANAGING USERS AND GROUPS 30 dC Configuration dr Queue s User statistics Number of users logged in 1 Number of logins 2 User Sessions a o Gi II aiaa Refresh Statistics 9 Audit log Figure 4 8 The user statistics user names have been blurred You can also log users off by expanding the user sessions on the sign and the click Invalidate Session This will open a confirmation dialog where you can also write a message to
56. h low overheads such as imports and trimming jobs and one for tasks with higher overheads such as de novo assemblies or read mappings 6 2 9 Testing a Grid Preset There are two types of tests that can be run to check a Grid Preset The first runs automatically whenever the Save Configuration button in the Grid Preset configuration window is pressed This is a basic test that looks for the native library you have specified The second type of test is optional and is launched if the Submit test job button is pressed This submits a small test job to your grid and the information returned is checked for things that might indicate problems with the configuration While the job is running a window is visible highlighting the jobs progression as shown in figure 6 7 Submit test job Submit a test job for the preset mytestpreset This will submit a job to the grid scheduler by using the library opt oge6_2u6 lib Ix24 x86 libdrmaa so and evaluate the output upon termination 3 22 11 12 53 PM external application GridTestExecuter External app External app Close Figure 6 7 Testing a Grid Preset 6 2 10 Client side starting CLC jobs on the grid Installing the CLC Workbench Client Plug in To submit jobs to the grid from within a CLC Workbench users must be able to access the CLC Science Server which means that the CLC Workbench Client Plug in must be installed in the Workbench as described in section 2 8 Starting grid job
57. hared directories identified in the Grid Preset s and any clcgridworker vmoptions files e Are your CLC Genomic Server file locations mounted with the same path on the grid nodes as on the master Genomics Server and accessible to the user that runs the CLC Genomics Server process e If you store data in a database are all the grid nodes able to access that database using the user account of the user running the CLC Science Server process e If you store data in a database did you enter a machine name in the Host box of the Database Location field when seeting up the Database Location using the CLC Science Server web administration form In particular a generic term such aS localhost will not work as the grid nodes will not be able to find the host with the database on it using that information e If you installed the CLC Science Server as root and then later decided to run it as a non privileged user please ensure that you stop the server recursively change ownership on the CLC Science Server installation directory and any data locations assigned to the CLC Server Please restart the server as the new user You may need to re index your CLC data locations section 3 2 2 after you restart the server e Is your java binary on the PATH If not then either add it to PATH or edit the clegridworker script in the CLC Science Server installation area with the relative path from this location gridres dist clcgridworker and set the JAVA varia
58. he CLC Workbench Client Plugin Then click in the button labelled Download and Install If you are working on a system not connected to the network then you can also install the plug in by downloading the cpa file from the plugins page of our website Reco elcbio cCom Cloplnala Then start up the Plug in manager within the Workbench and click on the button at the bottom of the Plug in manager labelled Install from File You need to restart the Workbench before the plug in is ready for use Note that if you want users to be able to use External applications see chapter 8 on the server there is a separate plug in CLC External Applications Plug in that needs to be installed in the Workbench the same way as described above In order to install plug ins on many systems the Workbench must be run in administrator mode On Windows Vista and Windows 7 you can do this by right clicking the program shortcut and choosing Run as Administrator Chapter 3 Configuring and administering the server 3 1 Logging into the administrative interface Once the server is running you can log into its administrative interface via a web browser Most configuration occurs via this interface Simply type the host name of the server machine you have installed the CLC Science Server software on followed by the port it is listening on Unless you change it the port number is f An example would be http clccomputer 7777 The default administive u
59. he job nodes and it needs to act as the same user when accessing the folder no matter whether it is a job node or a master node The data location should be added after the job nodes have been configured and attached to the master node In this way all the job nodes will inherit the configurations made on the master node One relatively common problem faced in this regard is root squashing which often needs to be disabled because it prevents the servers from writing and accessing the files as the same user read more about this athttp nfs sourceforge net ffaqg bl You can read further about job node setups in section 6 CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 21 3 2 2 Rebuilding the index The server maintains an index of all the elements in the data locations The index is used when searching for data For all locations you can choose to Rebuild Index This should be done only when a new location is added or if you experience problems while searching e g something is missing from the search results This operation can take a long time depending on how much data is stored in this location If you move the server from one computer to another you need to move the index as well Alternatively you can re build the index on the new server this is the default option when you add a location If the rebuild index operation takes too long and you would prefer to move the old index simply copy the folder called searchindex from t
60. he old server installation folder to the new server The status of the index server can be seen in the User Statistics pane showing information on where the index server resides and the number of locations currently being serviced 3 3 Changing the listening port The default listening port for the CLC Server is 7777 This has been chosen to minimize the risk of collisions with existing web servers using the more familiar ports 80 and 8080 If you would like to have the server listening on port 80 in order to simplify the URL this can be done in the following way Navigate to the CLC Server installation directory Locate the file called server xml in the conf directory Open the file in a text editor and locate the following section Connector port 777 protocol ATTP 1 1 connectionTimeout 20000 redirectPort 8443 gt Change the port value to desired listening port 80 in the example below Connector port 80 protocol HTIP 1 1 connectionTimeout 20000 redirectPort 8443 gt Restart the service for the change to take effect see how to restart the server in section 2 7 3 4 Changing the tmp directory The CLC Science Server often uses a lot of disk space for temporary files These are files needed during an analysis and they are deleted when no longer needed By default these temporary files are written to your system default temporary directory Due to the amount of space that can be required for temporary fi
61. he one that will be used 1 Any virtual memory settings given in the grid preset or if that is not set then 2 Any physical memory settings given in the grid preset or if that is not set then 3 Half of the total memory present with 50GB being the maximum set in this circumstance Please note that any nodes running a 32 bit operating system will have a maximum memory allocation for the java process of 1 2GB C binaries For the computationally intensive tools that include a phase using a C binary e g de novo assembly and jobs involving mapping phases e g read mappings RNA seq analyses smallRNA analyses etc the C binary phase is not restricted by the amount of memory set for the java process For this reason we highly recommend caution if you plan to submit more jobs of these types to nodes that are being used simultaneously for other work Chapter 7 BLAST The CLC Science Server supports running BLAST jobs Users will be able to submit BLAST jobs to be run on the Genomics Server they will be able to select data from Server data locations see section 3 2 1 to search against other sequences held in Server data locations or against BLAST databases stored in an area configured as an import export directory see section From a Workbench user s perspective they will see two categories of data to search against when they are setting up their BLAST job These are shown in figure 7 1 e Select from among the databa
62. he right by clicking Add Item see figure 5 7 g Manage attributes Attributes Attribute info Type List Name My list th Add Value db Add Attribute Remove Attribute 7 Fe Figure 5 7 Defining items in a list Remove items in the list by pressing Remove Item CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 37 5 3 3 Removing attributes To remove an attribute select the attribute in the list and click Remove Attribute This can be done without any further implications if the attribute has just been created but if you remove an attribute where values have already been given for elements in the data location it will have implications for these elements The values will not be removed but they will become static which means that they cannot be edited anymore They can only be removed see more about how this looks in the user interface below If you accidentally removed an attribute and wish to restore it this can be done by creating a new attribute of exactly the same name and type as the one you removed All the static values will now become editable again When you remove an attribute it will no longer be possible to search for it even if there is static information on elements in the data location Renaming and changing the type of an attribute is not possible you will have to create a new one 5 3 4 Changing the order of the attributes You can change the order of the attributes
63. iltering of the variant track The workflow is created in the CLC Workbench and an installer file is created that can be installed on the CLC Science Server For information about creating a workflow please see the user manual of CLC Genomics Workbench or CLC Main Workbench at http www clcbio com usermanuals 9 1 Installing and configuring workflows Workflows can be installed from the server web interface Admin 473 Workflows Click the Install Workflow button and select a workflow installer for information about creating a workflow please see the user manual of CLC Genomics Workbench or CLC Main Workbench at http www clcbio com usermanuals Once installed the workflow is listed with a validated d or attention 0 status icon as shown in figure 9 1 In this example there are several workflow elements that can be configured Simply click the box and you will see a dialog listing the parameters that need to be configured as well as an overview of all the parameters An example is shown in figure 9 2 In addition to the configuration of values for the open parameters you can also specify which of those open parameters that should be locked this means that the parameter cannot be changed when executing the workflow Learn more about locking and unlocking parameters in the user manual of CLC Genomics Workbench or CLC Main Workbench at http www clcbio com usermanuals 9 2 Executing workflows Once a workflow is installed
64. ing steps are taken to setup grid integration for CLC bio jobs These steps are described in more detail in the sections that follow It is assumed that your CLC Genomics Server software is already installed on the machine that is to act as the master 1 Set up the licensing of the grid workers as described in section 6 2 4 2 Configure the CLC grid licenses as a consumable resource in the local grid system as described in section 6 2 5 3 Configure and save grid presets as described in section 6 2 6 4 If not already done install the CLC Workbench Client Plugin in the Workbenches as described in section 2 8 to be used to submit jobs to your grid 5 Optionally create and edit a clegridworker vmoptions file in each deployed CLC Grid Worker area aS described in section 6 2 8 This is usually desirable and would be done if you wished to customize settings such as maximum memory to dedicate to the java process 6 Test your setup by submitting some small tasks to the grid via a CLC Science Server client such as the CLC Genomics Workbench or the Command Line Tools Ideally these would be tasks already known to run smoothly directly on your CLC Science Server CHAPTER 6 JOB DISTRIBUTION 4 6 2 4 Licensing of grid workers There are two main steps involved in setting up the licenses for your CLC Grid Workers Step 1 Installing network licenses and making them available for use Generally a pool of CLC grid licenses are purchased and ar
65. installation directory have the appropriate permissions The easiest way to do this is to recursively change the ownership of all the files in that directory to the user that will run the CLC Science Server process As a service On installation a link is created in etc init d to the CLCScienceServer script At this point you need to configure it as a service For example on Red Hat systems e service clcserver startupscript start We provide an example wrapper script for running the CLC Science Server process You may find this convenient if you plan to run the process as a user other than the root user The script is called clcserver startupscript and can be found under the conf directory of the CLC Science Server installation area Please refer to your operating system documentation if you require further information about setting up services on your system 2 8 Installing relevant plug ins in the Workbench In order to use the CLC Science Server from a CLC Workbench you need to install the CLC Workbench Client Plug in in the Workbench This plug in is needed for logging onto the server and accessing data from the server data locations Plug ins are installed using the Plug ins and Resources Manager which can be accessed via the menu in the Workbench Help Plug ins and Resources 221 or via the Plug ins 5 button on the Toolbar From within the Plug ins and Resources Manager choose the Download Plug ins tab and click on t
66. les it can be useful to specify an alternative larger disk area where temporary files created by the CLC Genomics Server can be written CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 22 In the server installation directory you will find a file called CLCScienceServer vmoptions Open this file in a text editor and add a new line like this Djava io tmpdir path to tmp with the path to the new tmp directory Restart the server for the change to take effect see how to restart the server in section 2 7 We highly recommend that the tmp area is set to a file system local to the server machine Having tmp set to a file system on a network mounted drive can substantially affect the speed of performance 3 4 1 Job node setups The advice about having a tmp area being set on a local file system is true also for job nodes Here the tmp areas for nodes should not point to a shared folder Rather each node should have a tmp area with an identical name and path but situated on a drive local to each node You will need to edit the CLCScienceServer vmoptions file on each job node as well as the master node as described above This setting is not pushed out from the master to the job nodes 3 5 Setting the amount of memory available for the JVM When running the CLC Science Server the Java Virtual Machine JVM needs to know how much memory it can use This depends on the amount of physical memory RAM and can thus be different from comput
67. lock is overlayed when the connection is encrypted via SSL 10 3 3 Enabling redirection from non ssl port to ssl enabled port If SSL is to be mandatory it is possible to get the non ssl port 7777 to forward to the ssl port 8443 rather than closing down the non ssl port This is done by adding the following section to the conf web xml file CHAPTER 10 APPENDIX 14 Untrusted Certificate The server localhost presented an unknown certificate with the following attributes Subject Common Name localhost Alternative names N A Organizational Unit Enterprise Organization CLC Bio Locality Aarhus N State N A Country DK Issuer Common Name localhost Organizational Unit Enterprise Organization CLC Bio Locality Aarhus N State N A Country DK Fingerprints SHA 1 Fingerprint A5 F6 8D C4 F6 F3 CB 44 DO BA 83 E9 36 14 AE 9B 68 9B 9C F9 SHA 256 Fingerprint 4B B5 OB 04 3C 3A A1 E2 D1 BF 87 10 F1 5D EA DD 9B 92 FF E3 C1 C9 9A 35 48 AF F6 98 87 SF 1D AB Validity Period Valid From Sep 1 2011 Valid To Aug 31 2012 Do you want to trust this certificate Figure 10 3 A warning is shown when the certificate is not signed by a recognized CA a 5 Idle Connected to localhostlocaldomain running CLC Genomics Server 3 2 1 as user root Connection is encrypted lick to view server s certificate Figure 10 4 Showing details on the server connection by placing the mouse on the globe lt security
68. mitter of the grid job and thus this user must exist on all the grid nodes e CLC Genomic Server file locations holding data that will be used must be mounted with the same path on the grid nodes as on the master Genomics Server and accessible to the user that runs the CLC Genomics Server process e f a CLC Bioinformatics Database is in use all the grid nodes must be able to access that database using the user that runs the CLC Genomics Server process e A CLC License Server with one or more available CLC Genomics Grid Worker licenses must be reachable from the execution hosts in the grid setup e A SUN Oracle Java Runtime environment 1 6 must be installed on all execution hosts that will be running CLC Grid Worker jobs Supported job submission systems The scheduling systems CLC officially supports are OGE and PBS Pro as these are the ones we have tested A few customers are successfully using the scheduling system LSF although to do so requires some reconfiguration of the scheduling system itself Please contact the CLC Support Team if you wish to use the LSF scheduling system for CLC jobs On a more general level e The grid integration in the CLC Genomics Server is done using DRMAA Integrating with any submission system that provides a working DRMAA library should be possible e The scheduling system must also provide some means of limiting the number of CLC jobs launched for execution so that when this number exceeds the number o
69. nector entry for port 7777 can safely be removed from the server xml file Self signed certificates can be generated if only connection encryption is needed See http www akadia com services ssh test certificate html for further details Creating a PKCS12 keystore file If the certificate is not supplied in a pkcs12 keystore file it can be put into one by combining the private key and the signed certificate obtained from the CA by using openssl openssl pkcs12 export out keystore pkcs1l2 inkey private key in certificate crt name tomcat This will take the private key from the file private key and the signed certificate from certificate crt and generate a pkcs12 store in the keystore pkcs12 file 10 3 2 Logging in using SSL from the Workbench When the Workbench connects to the CLC Science Server it automatically detects if Secure Socket Layer SSL should be used or not If SSL is detected the server s certificate will be verified and a warning is displayed if the certificate is not signed by a recognized Certificate Authority CA as shown in figure 10 3 When such an unknown certificate has been accepted once the warning will not appear again It is necessary to log in again once the certificate has been accepted When logged into a server information about the connection can be viewed by hovering the connection icon on the status panel as shown in figure 10 4 The icon is gray when the user is not logged in and a pad
70. nnections on this port before your clients can contact the server from a Workbench or web browser Consult the documentation of your firewall for information on how to do this Besides the public port described above the server also uses an internal port on 7776 There is no need to allow incoming connections from client machines to this port 2 6 Downloading a license The CLC Science Server will look for licenses in the licenses folder This means that all license files should be located in this folder Check the platform specific instructions below to see how to download a license file 2 6 1 Windows license download License files are downloaded using the downloadlicense command script To run the script right click on the file and choose Run as administrator This will present a window as shown in figure 2 4 ee C Windows System32 cmd exe TTT Ee Eee HH bio license download utility HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Hostname HostID s gt Please enter Cor copy paste your license Order ID and press return gt Em a Figure 2 4 Download a license based on the Order ID Paste the Order ID supplied by CLC bio right click to Paste and press Enter Please contact Support clcbio com if you have not received an Order ID Note that if you are upgrading an existing license file this needs to be deleted from the licenses folder When you run the downloadlicense command scrip
71. nstallation root The configure script expects to be able to find lib libpbs a and include pbs ifl h in the given root amongst other files SSL is needed The configure script expects that linking with ssl will work thus libssl so must be present in one of the system s library paths On Red Hat and SUSE you will have to install openssl devel packages to get that symlink or create it yourself The install procedure will install libdrmaa so to the provided prefix configure argument which is the file the CLC Science Server needs to know about The PBS DRMAA library can be configured to work in various modes as described in the README file of the pbs drmaa source code We have experienced the best performance when the CLC Server has access to the PBS log files and pbs drmaa is configured with wait thread 1 6 2 2 Technical overview Figure 6 5 shows an overview of the communication involved in running a job on the grid using OGE as the example submission system 4 Job is scheduled at a grid node 3 Job sumitted to Oracle Grid Engine Oracle Grid Engine hedule GridNode 5 Grid node reads job parameters and job data CLC Server 6 Result is written to shared network drive 1 User submits ane 2 Job parameters is transferred grid job to server to shared network drive Shared Network Drive SS e Figure 6 5 An overview of grid integration using OGE as the example submission system The steps of thi
72. o take effect Instead of 1 you write the maximum number of cores that the CLC Science Server is allowed to use Please note that this is not a guarantee that the CLC Science Server will never use more cores than specified but that will be for very brief and infrequent peaks and should not affect performance of other applications running on your system You can download a sample cpu properties fileathttp clcbio com files deployment cpu properties 3 1 Other configurations 3 7 1 HTTP settings Under the Admin are tab click Configuration and you will be able to specify HTTP settings Here you can set the time out for the user HTTP session and the maximum upload size when uploading files through the web interface 3 2 Audit log settings The audit log records all the actions performed in the web interface and through the Workbenches Note that data management operations copying deleting and adding files done through the Workbench are not recorded 3 3 Deployment of server information to CLC Workbenches See the Deployment manual at http www clcbio com usermanuals for information on pre configuring the server log in information when Workbench users log in for the first time 3 8 Server plug ins La You can install plug ins on the server under the Admin Ga tab see figure 3 2 SY Element Info CD History Sequence Text F Download Upload Main configuration Authentication Job nodes
73. orted 8 6 2 Running Velvet from the Workbench Next step is to test if it can actually be executed Open the Workbench with the External Applications Client Plug in installed Go to Toolbox CLC Server E External Applications gt You will now see a list of all the applications that have been set up figure 8 6 E Start server external application 1 Select the external application External applications CLC bio Velvet w Figure 8 6 Running Velvet from the Workbench In this case there is only one When you click Next you can select LO some sequences set a few parameters and click Next and Finish The process that follows has four steps 1 The sequencing reads are exported by the server to a fasta file The fasta file is a temporary CHAPTER 8 EXTERNAL APPLICATIONS 65 file that will be deleted when the process is done 2 The velvet script is executed using this fasta file and the user specified parameters as input 3 The resulting output file is imported into the save location specified in the save step of the Workbench dialog and the user is notified that the process is done 4 All temporary files are deleted 8 6 3 Understanding the Velvet configuration We will now explain how the configuration that we made actually works And hopefully this will make it possible for you to design your own integrations Going back to figure 8 5 there is a text field at the top This is where
74. ou are installing the server on a Windows system you will be able to choose if the service is started manually or automatically by the system CHAPTER 2 INSTALLATION 13 Select Destination Directory Where should CLC Genomics Server be installed Select the folder where you would like CLC Genomics Server to be installed then click Next Destination directory Applications CLCGenomicsServer Required disk space 108 1 MB Free disk space 19 835 MB install4j Figure 2 2 Choose where to install the server Setup CLC Genomics Server 3 6 Configure memory limit Select the amount of memory available to the CLC Server System Memory 7912 ME Maximum value 7912 MB The maximum possible value depends on your operating system amount of system memory and type of computer 32 bit or 64 bit _ Figure 2 3 Choose the maximum amount of memory used by the server The installer will now extract the necessary files On a Windows system if you have chosen that the service should be started automatically the service should also start running at this point Please note that if you do not already have a license file installed then the CLC Science Server process will be running in a limited capacity at this point Downloading a license is described in section 2 6 Information on stopping and starting the CLC Science Server service is provided in section 2 7 2 3 Silent installation
75. ource 6 2 6 Configure grid presets 6 2 Controlling the number of cores utilized 6 2 8 Other grid worker options 6 2 9 Testing a Grid Preset 6 2 10 Client side starting CLC jobs on the grid Installing the CLC Workbench Client Plug in Starting grid jobS 564 du we aw ww a 6 2 11 Grid Integration Tips 6 2 12 Understanding memory settings 7 BLAST 7 1 Adding directories for storing BLAST databases 35 35 36 37 37 37 39 39 40 41 41 41 42 43 44 44 45 46 47 48 48 50 91 52 52 52 52 52 54 55 CONTENTS 7 2 Adding and removing BLAST databases 2 0005 eeu 8 External applications 8 1 External applications integration Basic configuration 1 8 2 External applications integration Post processing 8 08 8 3 External applications integration Stream handling 0 6 8 4 External applications integration Environment 2 0 008 ee cc 8 4 1 Environmental Variables aww SA NE RENA EE Dita MOMME dlect ss soe Ge SS EDS RE DA A 8 4 3 Execute as master process 2 cs 8 5 External applications integration Parameter flow 1 a gt 8 6 External applications integration Velvet 0 0 eee ee ee eee ee Ba PEINE V VEE fea he Chae Gwe EEE E ee ee oe ee ES 8 6 2 Running Velvet from the Workbench 2 0 0 ee uve ve nae 8 6 3 Understanding the Velvet configuration 2 0 02 0 004s
76. ource 1 nodes 1 ppn X where X is the number of cores As this resource is alSo designed to work with parallel system the number of nodes is allowed to be larger than 1 For the sake of scheduling cores it is vital that this parameter is kept at 1 An example of a native specification is q bit32 1 nodes 1 ppn 2 which will request two cores and be queued in the bit32 queue 6 2 8 Other grid worker options Additional java options can be set for grid workers by creating a file called clcgridworker vmoptions in the same folder as the deployed clcgridworker script that is the clegridworker script within the folder specified in the Path to CLC GridWorker field of the grid preset For example ifa clcgridworker vmoptions was Created containing the following two lines it would for the CLC Grid Worker specified in a given preset set memory limits for the CLC Science Server java process and a temporary directory available from the grid nodes overriding the defaults that would otherwise apply Xmx1000m Djava io tmpdir path to tmp CHAPTER 6 JOB DISTRIBUTION 92 For each grid preset you created you can create a clcgridworker vmoptions file within the folder you specified in the Path to CLC GridWorker field So for example if you had two grid presets you could set two quite different memory limits for the CLC Science Server java process This might be a useful idea in the case where you wished to provide two queues one for tasks wit
77. pes of machines running the CLC Science Server 6 1 2 User credentials on a master job node setup If you have a brand new installation and you plan to use the default administrative login credentials See section 3 1 you do not need to change anything If you wish to set other authentication details then log into the web administration interface on each machine and set up identical authentication details on each one CHAPTER 6 JOB DISTRIBUTION 42 Server mode MASTER NODE Managing processing zN SINGLE SERVER One server all processing done locall MASTER_NODE Managing processing EXECUTION NODE Local processing onl Figure 6 2 The configuration options for the types of machines running the CLC Science Server The choices of relevance under normal circumstances are Single_server and Master_node An administrator will not usually need to manually choose the Execution Host option This option is there primarily to allow for troubleshooting You can now log out of the CLC Science Server web administrative interface on all the machines except the one that will be designated the master node All further configuration will take place on the machine to be the master node 6 1 3 Configuring your setup If you have not already please download and install your license to the master node See section 2 6 Do not install license files on the job nodes The licensing information including how many job nodes you are can run ar
78. red to hold BLAST database By default if you do not change any permissions within the CLC Genomics Server all users logging into the CLC Genomics Server e g via their Workbench or via the Command Line Tools will be able to create BLAST databases in the areas you have configured to hold BLAST databases If you wish to restrict the ability to create BLAST databases to these areas completely but still wish your users to be able to access the BLAST databases to search against then set the file system level permissions on the import export directory so they are read only When listing the databases as shown in figure 7 3 it is possible to delete the databases by clicking the Delete link in the right hand side Chapter 8 External applications Command line applications on the server machine can easily be made available via the graphical menu system of the Workbench Such third party applications can then be run via the normal graphical menu system of CLC Genomics Workbenches that are connected to the CLC Science Server These tools can access data on the machine the CLC Workbench is installed on data stored on the CLC Science Server or data stored in areas of the server accessible to the CLC Science Server depending on choices made by the server administrator The third party programs are executed on the server not the local Workbench giving the administrator full control over the execution environment The integration of third party
79. s Once the server side is configured and the CLC Workbench Client Plug in has been installed in the CLC Genomics Workbench an extra option will appear in the first dialogue presented when setting up a task that could be executed on the CLC Science Server Users will be able to choose to execute such a task on their local machine the CLC Server machine or using any available grid presets To submit to the grid is as simple as choosing from among the grid presets in the drop down box See figure 6 8 6 2 11 Grid Integration Tips If you are having problems with your CLC Grid Integration please check the following points CHAPTER 6 JOB DISTRIBUTION 53 1 Choose where to run Miss inanan J Workbench CLC Server Grid Submit to long queue lt Submit to long queue Submit to medium queue Submit to very long queue N Figure 6 8 Starting the job on the grid 9 gt Next AX Cancel e Does your system meets the requirements of the CLC Grid Integration Tool 6 2 1 For example please check that the machine the CLC Science Server is running on is configured as a submit host for your grid system and please check that you are running Sun Oracle Java 1 6 on all execution hosts e The user running the CLC Science Server process is the same user seen as the submitter of all jobs to the grid Does this user exist on your grid nodes Does it have permission to submit to the necessary queues and to write to the s
80. s figure are in detail CHAPTER 6 JOB DISTRIBUTION 46 1 From the Workbench the user invokes an algorithm to be run on the grid This information is sent to the master server running the CLC Science Server 2 The master server writes a file with job parameters to shred work directory of the grid execution nodes The job parameters contain identifiers mapping to the job data placed in the CLC server data location The job parameters file is automatically deleted when it is no longer used by the grid node 3 Now the server invokes qsub through the specified DRMAA native library Then qsub transfers the job request to the grid scheduler Since the user that runs the CLC Server process has invoked qsub the grid node will run the job as this CLC Server user 4 The job scheduler will choose a grid node based on the parameters given to qsub and the user that invoked qsub 5 The chosen grid node will retrieve CLC Grid Worker executable and the job parameters from the shared file system and start performing the given task 6 After completion of the job the grid node will write the results to the server s data location After this step the result can be accessed by the Workbench user through the master server 6 2 3 Setting up the grid integration CLC jobs are submitted to a local grid via a special stand alone executable called clegridworker In the documentation this executable is also referred to as the CLC Grid Worker The follow
81. s on a local network The default configuration of the server does not use SSL 10 3 1 Enabling SSL on the server A server certificate is required before SSL can be enabled on the CLC Science Server This is usually obtained from a Certificate Authority CA like Thawte or Verisign see http en wikipedia org wiki Certificate_authorities A signed certificate in a pkcs12 keystore file is also needed The keystore file is either provided by the CA or it can be generated from the private key used to request the certificate and the signed certificate file from the CA see section 10 3 1 Copy the keystore file to the conf subdirectory of the CLC Science Server installation folder CHAPTER 10 APPENDIX 3 Next the server xml file in the conf subdirectory of the CLC Science Server installation folder has to be edited to enable SSL connections Add text like the following text to the server xml file lt Connector port 8443 protocol HTTP 1 1 SSLEnabled true maxThreads 150 scheme https secure true clientAuth false sslProtocol TLS keystoreFile conf keystore pkcs12 keystorePass tomcat keystoreType PKCS12 J gt Replace keystore pkcs12 with the name of your keystore file and replace tomcat with the password for your keystore The above settings make SSL available on port 8443 The standard non SSL port would still be TTT or whatever you may have configured it to If only SSL connection should be allowed the con
82. s to an element can be saved Save Eh and new elements and subfolders can be created For a user to be able to access a folder there has to be at least read access to all the top folders In the example shown in figure 5 1 to access the Sequences folder the user must have at least read access to both the Example Data and Protein folders 31 CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 32 a Example Data E Cloning vectors EJ Extra L la Nucleotide E Protein EF 3D structures HJ More data Ea ISequences e LPM 1A29 HUMAN e r CAA24102 e LPM CAAS2Z220 e fe NP 058652 Fh Ps04o e ys P6s053 e lth PhoDos e lth P6225 ov LPM DG Z 25 Figure o 1 A folder hierarchy on the server e EEE EM F I jj i Oe T However you can grant read access to the Example Data and Protein folders and only grant write access to the Sequences folder Permissions on file system locations must be explicitly enabled if they are desired see section 3 2 1 Please see 5 1 2 for further details about the system behaviour if permission are not enabled and configured If permissions are enabled on a file system location then by default no groups have read or write access to any area under this location until permissions are configured Only the CLC Science Server root user will have access to the data held in the server at this point In other words you must set permissions on folders in this file system location before any users will
83. se see your grid scheduling documentation to determine what options are available for your scheduling system Example 1 To redirect standard output and error output you might put the following in the Native Specification field o lt path to standard out gt e lt path to error_out gt This corresponds to the following qsub command being generated qsub my script o lt path to standard out gt e lt path to error out gt Example 2 Use a specific OGE queue for all jobs hard 1 aqname lt name of queue gt This corresponds to the following qsub command gsub my script q queue name f x adding variables evaluated at run time Grid Presets are esentially static in nature with most options being defined directly in the preset itself In some cases though it may be of interest to have variables that are evaluated at runtime Currently three such variables can be added to the Native Specification line CHAPTER 6 JOB DISTRIBUTION 50 USER_NAME The name of the user who is logged into the server and is submitting the analysis request All grid jobs are submitted by the user that runs the CLC Server process so this variable might be added to for example log usage statistics for actual users of the system or to send an email to the an email account of a form that includes the contents of this variable For example the type of text that follows could be put into the Native specification field M_ USER_NAME Qyourmailserver com C
84. ser credentials are username root password default Use these details the first time you log in 3 2 Adding locations for saving data Before you can use the server for doing analyses you will need to add one or more locations for storing your data 3 2 1 Adding a file system location Under the File system locations heading click the Add New File Location button to add a new file system location see figure 3 1 In this dialog enter the path to the folder you want to use for storing the data The path should point to an existing folder on the server machine and the user running the server process needs to have read and write access to the folder This is usually a dedicated user or it may be the system s root user if you have not created a dedicated user for this purpose The file location s configured on the server will be accessible to those working using CLC Workbenches after they log into the server via their Workbench Once you have pressed Save Configuration learn more about rebuilding the index in section 3 2 2 this location will be added and it should now appear in the Navigation Area in the left 19 CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 20 Path mnt data clc_data Permissions enabled Rebuild index when adding location recommended Figure 3 1 File system location settings hand side of the window By default it will also appear in the Workbench on next login You can use the checkbo
85. ses and list them under the BLAST tab in the web interface see a section of 55 CHAPTER 7 BLAST 56 1 Choose where to run NSet parame te 2 Select sequences of same type 3 Choose program and target BLAST program Program blastn DNA sequence and database Target gt Sequences BLAST database vector DNA vector Add as BLAST Location Save Cancel Figure 7 2 Adding import export directories as BLAST database locations this as an example in figure 7 3 This overview is similar to the one you find in the Workbench BLAST manager for local databases including the following in formation Name The name of the BLAST database Description Detailed description of the contents of the database Date The date the database was created Sequences The number of sequences in the database Type The type can be either nucleotide DNA or protein Total size 1000 residues The number of residues in the database either bases or amino acid Location The location of the database CHAPTER 7 BLAST of 9 BLAST Databases BLAST databases overview Name Description Date Sequences Type NC 000001 Human makeDB test 2011 11 14 19 DNA all_contig Homo sapiens build 37 3 genome database 2011 10 07 4900 DNA reference assembly GRCh37 p5 6CF_000001405 17 and alternate assemblies HuRef GCF_000002125 1 and CRA_TCAGchr v2 GCF_000002135 2 allcontig_and_rna mouse build 37 RNA reference and alternate 2
86. ses located on the Server This option is described in detail below e Select sequences from the Navigation Area to search against Here users choose from data stored in a Server data location A temporary database is then created from that data in your Server temp area see section 3 4 Once the BLAST job is complete temporary blast databases are deleted 1 4 Adding directories for storing BLAST databases In the web interface of the server you can configure your Server for BLAST databases Admin 3 BLAST 73 Here you can add a folder where you want the Server to look for BLAST databases Any folder used for BLAST databases accessible to the CLC Science Server must already have been configured as an import export directory see section This is a different situation than for other algorithms where the data is stored in data locations This difference is because BLAST databases are not truly CLC data and thus are stored outside data locations specified for CLC data They still need to be stored somewhere accessible to the Genomics Server process though hence the need to put them in a directory configured as an import export directory Clicking Edit BLAST Database Locations will bring up a dialog as shown in figure 7 2 where you can select which of the import export directories you wish to use for storing BLAST databases Once added as a BLAST Database Location the CLC Science Server will search this directory for any BLAST databa
87. setting up this model are to 1 Install the CLC Science Server software on all the machines involved See section 2 2 2 Start up the CLC Science Server software on all the machines involved See section 2 7 3 Install the license on the machine that will act as the master node See section 2 6 4 Log into the web adminstrative interface for the CLC Science Server of the machine that will act as the master node See section 3 1 5 Configure the Master node and the job nodes via the administrative interface on the Master node The only work you have to do directly on the machines that will run as job nodes is to install the CLC Science Server and start the software up on each of them Almost all other configurations are done via the web adminstrative interface for the CLC Science Server of the master node This includes the installation of plug ins See section section 0 1 4 6 1 1 Master and job nodes explained A machine running the CLC Science Server software can be considered to be of one of three types 1 Single server a server to which users submit jobs and which runs those jobs 2 Master node a machine that accepts jobs from users and then passes them to other systems either to execution nodes see below or a local grid system 3 Execution node here used to describe a machine running the CLC Science Server that accepts jobs directly from a Master node Figure 6 2 shows the configuration options for the ty
88. ssword default section 3 Change the root password section 4 1 Configure authentication mechanism and optionally set up users and groups section 4 2 Add data locations section 3 2 Download and install plug ins in the Workbench needed for the Workbench to contact the server section 2 8 Check your server set up using the Check set up link in the upper right corner as described in section 10 1 1 Your server is now ready for use Installing and running the Server Getting the CLC Science Server software installed and running involves at minimum these steps 11 CHAPTER 2 INSTALLATION 12 1 Install the software 2 Ensure the necessary port in the firewall is open 3 Download a license 4 Start the Server and or configure it as a service All these steps are covered in this section of the manual Further configuration information including for job nodes grid nodes and External Applications are provided in later chapters Installing and running the CLC Science Server is straightforward However if you do run into troubles please refer to the troubleshooting section in Appendix 10 1 which provides tips on how to troubleshoot problems yourself as well as how to get help 2 2 1 Installing the Server software The installation can only be performed by a user with administrative privileges On some operating systems you can double click on the installer file icon to begin installation Depending on
89. supplied information which has been entered in the Element info is attached to the attributes that have been defined in this particular data location If you copy the sequence to another data location or to a data location containing another attribute set the information will become fixed meaning that it is no longer editable and cannot be searched for Note that attributes that were Not set will disappear when you copy data to another location If the sequence is moved back to the original data location the information will again be editable and searchable 5 4 2 Searching When an attribute has been created it will automatically be available for searching This means that in the Local Search AR you can select the attribute in the list of search criteria see figure 5 11 Add filter Any Field gth Figure 5 11 The attributes from figure 5 8 are now listed in the search filter It will also be available in the Quick Search below the Navigation Area press Shift F1 and it will be listed see figure 5 12 Q Wildcard search Search related words Include both terms AND Include either term OR Any field search contents E E gt gt Me wa eae TARDE EEE F Name search name Length search length START TO END Organism search organism H E E Research_project search Research project Hyperlink search Hyperlink Location search Location Is
90. sword for selected user Set Password Remove selected user Remove User gt Manage groups Figure 4 3 Managing users 4 2 2 Managing groups using the web interface To create or remove groups or change group membership for users Admin 47 Users and groups e Manage groups This will display the panel shown in figure 4 4 Users and groups K Manage groups Create new group admin en selected g Remove Group T membership Users Group members gt Figure 4 4 Managing users The same user can be a member of several groups Note that membership of the admin group is used for allowing users access to the admin part of the web interface Users who should have access to the administrative part of the server should CHAPTER 4 MANAGING USERS AND GROUPS 28 be part of the admin group which is the only special group this group is already created for you Note that you will always be able to log in as root with administrative access The functionality of this plug in depends on the user authentication and management system if the built in system is used all the functionality described below is relevant if an external system is used for managing users and groups the menus below will be disabled 4 3 User authentication using the Workbench Users and groups can also be managed through the Workbench note that you need to set up the authentication mechanism as described in section 4
91. t it will create a new license file Restart the server for the new license to take effect see how to restart the server in section 2 7 1 2 6 2 Mac OS license download License files are downloaded using the downloadlicense command script To run the script double click on the file This will present a window as shown in figure 2 5 CHAPTER 2 INSTALLATION 16 BAR Terminal bash 79x24 bash macbook 1 gt qandersen S H H HE H H H HE HE1 HE E 1 HE HE11 HE 4 1 H 1 HE1 1 H 1 1 1 HE1 HE H H HA1 HE1 1 H 1 HE H 1 H 1 H H CLC bio License download utili ty HH HHHH H H H H H H H H H HH H E HH H H H H H H H H H HR H H RH H HRH Please enter for copy paste your License Order ID and press return Figure 2 5 Download a license based on the Order ID Paste the Order ID supplied by CLC bio and press Enter Please contact support clcbio com if you have not received an Order ID Note that if you are upgrading an existing license file this needs to be deleted from the licenses folder When you run the downloadlicense command script it will create a new license file Restart the server for the new license to take effect see how to restart the server in section 2 7 2 2 6 3 Linux license download License files are downloaded using the downloadlicense script Run the script and paste the Order ID supplied by CLC bio Please contact support clcbio com if you have not received an Order ID Note that if you are upgr
92. t k Standard error handling Anything on standard error is shown as user error dialog and execution is stopped Do not stop execution or show error dialogs Do notimport Figure 8 3 Stream handling Basically you can choose to ignore it or you can import it using one of the importers available on the server For some applications standard out produces the main result so here it makes sense to choose an appropriate importer But also for debugging purposes it can be beneficial to import standard out and standard error as text so that you can see it in the Workbench after a run CHAPTER 8 EXTERNAL APPLICATIONS 62 8 4 External applications integration Environment 8 4 1 Environmental Variables This section is still being written 8 4 2 Working directory Define the area where temporary files will be stored The Default temp dir option uses the directory specified by the java io tmpdir setting for your system The Shared temp dir option allows you to set one of the directories you have already specified as an Import export directory as the area to be used for temporary files created Choosing the Shared temp dir option means that temporary files created will be accessible to all execution nodes and the master server without having to move them between machines In contrast for a setup with CLC execution nodes that chooses the Default temp dir setting where such a directory is usually not shared between machines files will be moved
93. the plugin is enabled for each job node you wish to make available for users to run that particular task on To do this e Go to the Job Distribution tab in the master nodes web administrative interface e Click on the link to each job node e Click in the box by the relevant task marking it with a check mark if you wish to enable it CHAPTER 6 JOB DISTRIBUTION 44 6 2 Model Il Master server submitting to grid nodes The CLC Grid Integration Tool allows jobs to be offloaded from a master server onto grid nodes using the local grid submission queuing software to handle job scheduling and submission At the moment a given CLC algorithm will run on a single machine That is a single job will run on one node A single job is not distributed across nodes Thus each grid node employed for a given task must have enough memory and space to carry out that entire task 6 2 1 Requirements for CLC Grid Integration e A functional grid submission system must already be in place Please also see the section on supported job submission systems below e The DRMAA library for the grid submission system to be used Note that OGE comes with this library while you will need to get the code for the PBS DRMAA library and compile this yourself Additional notes below e The CLC Science Server must be installed on a Linux based system configured as a submit host in the grid environment e The user running the CLC Science Server process is seen as the sub
94. the user that will be displayed either in the Workbench or the browser Chapter 5 Access privileges and permissions The CLC Science Server allows server administrators to control access to the server on several levels e Access to the data in the server s data locations This is typically to allow groups of users to store data that cannot be accessed by other users or to establish reference data sources that are read only for most users e Access to running jobs on the server Particular groups of users can be restricted to running only particular types of jobs on the server e Access to the import export directories The server administrator can give users access to browsing designated directories on the server file system Thus it can be desirable to restrict this access to certain groups of users for security reasons The following sections describe each of these levels 5 1 Controlling access to data The CLC Science Server uses folders as the basic unit for controlling access to data and access is granted or denied to groups of users On any folder within a location you can grant two kinds of access to a group Read access This will make it possible for the users of the group to see the elements in this folder to open them and to copy them Access can be through any route for example browsing in the Navigation Area searching or clicking originates from in the History Ci of e g an alignment Write access Change
95. tions 10 2 1 Configurations for MySQL For MySQL we recommend basing your configuration on the example configuration file my large cnf which is included in the MySQL distribution In addition the following changes should be made The max_allowed_packet should be increased to allow transferring large binary objects to an from the database This is done by setting the option max_allowed_packet 64M InnoDB must be available and configured for the MySQL instance to work properly as the CLC Database You should enable the options in the InnoDB section of your configuration as suggested below 7 YOU Gan Sel butter pool size vp to 50 60 of RAM but beware of setting memory usage too high innodb_buffer_pool_size 256M innodb_additional_mem_pool_size 20M Set log file size to 25 of buffer pool size innodb log file size 64M innodb log buffer size 8M innodb flush log at trx commit 1 innodb lock wait timeout 50 There appears to be a bug in certain versions of MySQL which can cause the cleanup of the query cache to take a very long time some time many hours If you experience this you should disable the query log by setting the following option query cache size 0 10 3 SSL and encryption The CLC Science Server supports SSL communication between the server and its clients e g Workbenches or the CLC Server Command Line Tools This is particularly relevant if the server is accessible over the internet as well a
96. users as well CHAPTER 9 WORKFLOWS 69 References Single genome track or reference Add Remove References sequences Settings locked by creator Create report Auto detect paired distances track Annotation track Masking mode NO_MASKING EXCLUDE INCLUDE Collect un mapped reads 1 lt x lt 3 No masking Non specific match handling RANDOM IGNORE Color space alignment Map randomly Figure 9 2 The reference sequence is the only parameter that can be configured for the read mapping Y K Gene and Protein Analysis Y S Lab Work Support Sl Simple variant detection and annotation H E NGS Core Tools m f De Nove Sequencing Figure 9 3 A workflow is installed and ready to be used E Simple variant detection and annotation Workbench O CLC Server Grid oge nightly branch Remember setting and skip this step ra Jeo Xo Figure 9 4 Selecting where to run the workflow Chapter 10 Appendix 10 1 Troubleshooting If there are problems regarding the installation and configuration of the server please contact Support clcbio com 10 1 1 Check set up In order to check that your server has been set up correctly you can run the Check set up tool Log in on the web interface of the server as an administrator and click the Check Set up link at the upper right corner This will show a dialog where you click Generate Diagnostics Report This will show a list of test th
97. w a certain number of sessions i e number of log ins from e g the web interface or the workbench The number of sessions is part of the agreement with CLC bio when you purchase a license e A Special license if you are running the server on a grid system this is explained in detail in section 6 2 4 e A license for the workbench The Workbench is needed to start analyses on the server and view the results Find the user manuals and deployment manual for the Workbenches at http www clcbio com usermanuals CHAPTER 1 INTRODUCTION 10 The following chapter on installation will give you more information about how to obtain and deploy the license for the server Chapter 2 Installation 2 1 Quick installation guide The following describes briefly the steps needed to set up a CLC Science Server 2 2 with pointers to more detailed explanation of each step If you are going to set up execution nodes as well please read section 6 first 1 Ol Oo O N O 10 11 2 2 Download and run the server installer As part of the installation choose to start the server section 2 2 Run the license download script that is part of the installation section 2 6 The script will automatically download a license file and place it in the server installation directory under licenses Restart the server section 2 7 Log in to the server using a web browser note that the default port is 7 77 with username root and pa
98. w of the external applications integration The best way to describe the integration of third party command lines tools is through a series of examples We start with a very basic example and work towards more complex setups 8 1 External applications integration Basic configuration Many aspects of configuring external tools in the CLC Science Server can be described as we set up avery simple command We have chosen the cp command as will already be on your server The cp command requires at minimum two parameters an input file and an output file These parameters are positional the first filename given after the command is the input file the second is the output file Here we will just copy a fasta file from one place in the CLC Science Server to another This is a very inefficient way of doing this task but it will illustrate how to integrate a command line tool without requring you to install additional software on your system Under the External Applications tab of the CLC Science Server administrative web interface click on the New configuration button This brings up a window like that shown at the left side of figure 8 2 In the text box labeled External applications command name enter a name for this command This will be what the end user sees in the menu option they will be presented with via the Workbench In the text box labeled command line argument provide the command line Start CHAPTER 8 EXTERNAL APPLICATIONS 60 with the
99. x next to the location to indicate whether it should be visible to your users or not You can choose whether access control should be switched on and off Please see section 5 1 for more information about enabling and setting permissions on CLC Science Server data folders Note that pressing Remove Location will only remove the location from this list it will not delete the folder from your system or affect any data already stored in this folder The data will be accessible again simply by adding the folder as a new location again Important points about the CLC Server data in the file system locations Any file system locations added here should be folders dedicated for use by the CLC Science Server Such areas should be directly accessed only by the CLC Science Server In other words files should not be moved into these folders or their subfolders manually for example using your standard operating system s command tools drag and drop and so on All the data stored in this areas will be in clc format and will be owned by the user that runs the CLC Science Server process File locations for job node set ups When you have a job node set up all the job node computers need to have access to the same data location folder This is because the job nodes will write files directly to the folder rather than passing through the master node which would be a bottleneck for big jobs Furthermore the user running the server must be the same for all t

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