User manual CLC Server Command Line Tools
Contents
1. CLC Server Command Line Tools User manual Manual for CLC Server Command Line Tools 1 7 Windows Mac OS X and Linux March 8 2013 This software is for research purposes only CLC bio Finlandsgade 10 12 DK 8200 Aarhus N Denmark tC bio Contents 1 Introduction 4 L MASON txt a A E E a A RRA 1 2 System FEQUIFEMENES s i au a a ew A tee a 5 2 Basic usage 6 Zl Handing Passwords ao ica RE A a ea 7 2 2 Refenmine to nes the CLG URL os scs kia ar a e ae 9 2 2 1 Data on your local system occasion 9 2 22 Data Oli MES SENE o c so Gob ect a a a e ra 9 2 3 Result files and connecting analyses in pipelines o 10 2 2 EXCCUUIME WOLKNOWS o x05 aii oa e as de od dd ide 12 3 Example script 13 4 Usage for all commands 16 Chapter 1 Introduction Welcome to the user manual of CLC Server Command Line Tools The CLC Server Command Line Tools is a command line client for the CLC Genomics Server It is able to start analyses on the server import and export data and perform various data operations such as moving renaming and deleting data on the server A typical work flow using the CLC Server Command Line Tools might be 1 Import your sequence data 2 Run analyses such as read mapping SNP detection or RNA Seq 3 Optionally export the results to your local disk Another client available to run tasks on the CLC Genomics Server is the graphical CLC Genomics Workbench Below are recommendations for choo2. expected to be returned If this is not the number of results files that match the search string the command will return with exit code 10 This option is designed for use in scripts where you will wish to carry out validation steps are you proceed through the pipeline On the command line you check the error code returned by the previous command by typing echo C lt integer gt Specifies the column width of the help output 2 4 Executing workflows It is possible to execute workflows installed on the server Workflows are described in detail in the user manual of of CLC Genomics Workbench and CLC Genomics Server at http www clcbio com usermanuals Executing workflows is similar to executing algorithms and the installed workflows will be listed when the A is omitted Parameters that are open for change on execution are displayed when the workflow is specified for the A option Please note that the parameter names have name of the workflow element pre pended to make sure they are always unique Chapter 3 Example script In this section we present an example script showing a typical work flow consisting of the following steps e Import of NGS data e Read mapping e Variant detection The result of the variant detection is then exported to the local file system in Excel format The script is intended only as an example Hopefully it will be possible for you to modify it to fit your purposes You can download the script
3. interpreted by the CLC Server Command Line Tools when logging onto the server The token is encrypted and saved with the user profile on the computer running the CLC Server Command Line Tools You can generate a password token using the following command clcserverkeystor generat You will be prompted for the password After you have typed the password press the Enter key The password token is then returned on screen It will be a long string of text that you should save somewhere to refer to for future use So if we say that user bob has password secret and has generated a password token CATHMAAAAAAAAAPcb769377f4 then he could enter either of the following two commands to connect to his server The first passes the password in plain text The second passes it as an encrypted token CHAPTER 2 BASIC USAGE cleserver S server com U bob W secret clcserver S server com U bob W CAIHMAAAAAAAAAPcCb769377 4 If the token needs to be deleted the clcserverkeystore program has two other parameters that can be used d lt token gt This will delete the individual token provided as a parameter deleteAll This will delete all the tokens in the user profile The first section of the diagram below illustrates the process of logging into the server using a clear text password The second section illustrates the process of generating a password token and storing it in the keystore followed by a section showing how the tok
4. TH WORKFLOW SCRIPT 44E 4E dE AE AE AE AE AE AE AE FE FE FE FE FE FE FE FE E E E E E E E E E HE AE FE FE FE FE FE FE FE FE FE FE AE AE AE FE FE FE FE FE FE FE FE FE TE AE FE E E E E E E E AE AE AE AE HH FE FE FE FE FE HHH Make a directory for DIR echo we echo Make a directory DIR SSERVERCMD A mkdir t DATAPATH n DIR O tmpdir_result txt check_return_code make dir tmpdir PARSECMD f tmpdir_result txt c clc example check_return_code make dir result parsing rm tmpdir_result txt Make subdirectory in DIR folder for result and data echo we echo Make subdirectory SUBDIR SSERVERCMD A mkdir t tmpdir n S SUBDIR O mkdir_result txt check_return_code Make sub dir destdir PARSECMD f mkdir_result txt p d c SSUBDIR CHAPTER 3 EXAMPLE SCRIPT 15 check_return_code Make sub dir result parsing rm mkdir_result txt Import solid data echo we echo Import solid data SSERVERCMD A ngs_import_solid f SIMPORTPATH solid_matepair_F3 csfasta f SIMPORTPATH solid_matepair_F3 _ check_return_code Import solid data soliddata SPARSECMD f ngs_import_solid_result txt p i c solid ignorelog true check_return_code Import solid data result parsing rm ngs_import_solid_result txt Import genome echo we echo Import genome SSERVERCMD A import f automaticimport s SIMPORTPATH reference fa destdir O import_result txt check_return_code Import genome ref
5. ach command is also available in the online manual at http www clcsupport com clcservercommandlinetools current index php manual Usage_all_commands html An optional flag when working on the command line but important when working with scripts is 0 lt filename gt The name of a file to be created to hold a summary of steps carried out on the server and data locations of the results generated The data locations are of a form that can be used by downstream CLC commands See section 2 3 for information about parsing this file By default this file is placed in your working directory If you do not provide this flag this data will be written to a file called results txt For those working with the CLC Grid Integration Tool you can run import and algorithm commands through your grid nodes by adding the following flag to your clcserver command G lt grid preset name gt Other optional flags available for the cleserver command are C lt integer gt Specify the column width of the help output D lt boolean gt Enables debug mode when set to true providing more elaborate output and error messages H Display general help instructions V Display the version number of CLC Server Command Line Tools 2 1 Handling passwords To help you avoid sending your server login password in clear text across the network we provide the clcserverkeystore tool This enables you to convert your password to a token which is stored and can be
6. antage of using IDs over the path to the file is that the ID of the data remains the same even if the data object is renamed or moved If you wish to work with data IDs on the command line you can be easily get these using the Workbench See figure 2 1 IDs of data locations look something like this BAAAAAAPc132 7fff 268177574 7ff f The first part of this example ID gives the data location BAAAAAAPc132 7 f and this is followed by the ID for the file 268177574 7 f Files ready for upload to the CLC Genomics Server You can also use data files residing on the same machine as the CLC Server but not yet imported into a CLC Server File Location for particular functions e g import Such data needs to be in a CHAPTER 2 BASIC USAGE 10 location that the Server is allowed to access Such areas known as Import Export directories must be explicitly specified by the CLC Server administrator via the web administration interface To use data in one of these areas the serverfile version of a CLC URL is provided clc serverfile For example e clc serverfile mnt data project1 s_1 _1 sequence txt This refers to a file located on the same machine as the CLC Genomics Server the full path to the file is mnt data project1 s_1_1 sequence txt Note It is important not to put raw data or any other non CLC files into a directory designated as a CLC Server File Location or any of its subdirectories using standard system
7. data SPARSECMD f import_result txt p references c reference check_return_code Import genome result parsing rm import_result txt Do readmapping echo we echo Read Mapping SSERVERCMD A read_mapping soliddata destdir refdata O read_mapping_result txt check_return_code Read Mapping echo PARSECMD f read_mapping_result txt p i c mapping readmap SPARSECMD f read_mapping_result txt p i c Reads check_return_code Read Mapping result parsing rm read_mapping_result txt Quality based Variant Detection echo we echo Quality based Variant Detection SSERVERCMD A quality based_variant_detection create table true min coverage 1 variant in forward rever check_return_code Quality based Variation Detection table SPARSECMD f quality_result txt p s c Reads check_return_code Quality based Variation Detection result parsing rm quality_result txt Export variant table to excel echo we echo Export variant table to excel SSERVERCMD A export e excel_2010_exporter d table O table_export_result txt check_return_code Export variant table to excel file SPARSECMD f table_export_result txt O File check_return_code Export variant table to excel result parsing rm table_export_result txt Workflow completed echo we echo Workflow completed succesfully echo Variant table file Chapter 4 Usage for all commands A complete overview of
8. en is substituted by the CLC Server Command Line Tools with the real password when initiating the connection to the server host server com PES SSS SSS user bob HSSSS RRE ae F port 7777 Command password secret USER bobs LEA gt Line l AA AAA gt server com 7777 password secret Tool 4 4 Password token generation 4 generate 2 Set password secret Command Line Tool PA xxx password key xxx E NE Se CAIHMAAAAAAAAAPcb769377f4 hese Sse aos KR KR KR Rk 22 3 KeyStore 4 Password token invocation host server com port 7777 user bob She RSH Ste SSH Ss password Command user bob PERSE SSR RSE ESE SSA CAITHMAAAAAAAAAPcbh7 Line password secret 6937784 O gerea besos gt Tool 0 SSP SHS sees gt server com 7777 Ho l Pelee E 4 CHAPTER 2 BASIC USAGE 9 2 2 Referring to files the CLC URL Most commands will refer to data stored in files For some tasks such as importing or exporting the files may be on your local computer system For other tasks like running analyses the data may already be uploaded to the CLC server 2 2 1 Data on your local system Certain commands in particular import and export commands will require you to provide files on your local system Here you need only provide the relative or full path to the file or directory of interest on y
9. enerated after running the the trim algorithm using a sequence list called reads as input The result file lists the three files that were produced CHAPTER 2 BASIC USAGE 11 if Name reads trimmed lcUrl cle 127 0 0 1 7777 268177574 YCAAAAAAAAAAAAP c67 3b0db8c5e724f 5d66a991 12d75090d93 7ffFE ame reads report lcUrl clc 127 0 0 1 7777 268177574 ADAAAAAAAAAAAAPC673b0db8c5e724f 5d66a991 12475090d93 7fff p me Trim Sequences log lcUrl cle 127 0 0 1 7777 26817757 4 CAAAAAAAAAAAAAP C67 3b0db8c5e724f 5d66a991 12d75090d93 7ffF SHA 2 Ss SQ SS SO When creating pipelines stitching together several analyses you parse the result file to get the location of the data produced which is needed as input for the next algorithm The result file is just a text file but it can still be a challenge to parse it to get the necessary CLC URLs Thus we provide a tool called clc_result_parser to help with this It searches the result file for a text expression you provide and returns the CLC URL for files where a match to that text has been found in the Name field The Name field will contain the name of the input data along with a description of the type of data held in that file location In the case above you would probably search for the trimmed reads to use for further analysis which could be done with a command like this clcresultparser f result txt c trimmed Here the followin
10. g text would be returned cle 127 0 0 1 7777 268177574 YCAAAAAAAAAAAAP C67 3b0db8c5e724f 5d66a991 12d75090d93 7f fF The options for the clcresultparser program are f lt name of result file to parse gt This option is required c lt text to search for gt Text to search for in the Name field of the result file If nothing is found the exit code is 1 n lt text that should not match gt Text that should not be contained in the Name field of the result file r lt regexp gt A Java regular expression used for matching the name of the output See http java sun com docs books tutorial essential regex index html ignorelogs lt boolean gt By default all analyses produce log files You can provide false as the argument to this option to stop log files from being returned This is equivalent to excluding all names ending with log or log with a number suffix The latter are generated when there is more than one log file in the same folder p lt prefix text gt When more than one match is found the data locations for all matches will be output as a space separated list By supplying a prefix string you can stipulate what character s to separate the list using E g If you need to send several files output by the clcresultparser command as arguments to i options for the next analysis simply provide i as as the argument for the p flag CHAPTER 2 BASIC USAGE 12 e lt integer gt The number of CLC URLs that are
11. including data from http www clcbio com files CLCServerCommandLineTools 1 7 example workflow zip This is a shell script that will run on Linux and Mac OS bin bash HERE FE HERE EEE EE FE FE FE AE HEE HE EEE HE FE FE AE EEE EEE EHH EE EH REE ERE HE FE FE AE EE REE ATARI Example workflow script for CLC Server Command Line Tools 1 6 CLC bio June 2012 Se For full documentation please visit http clcbio com usermanuals e SETTINGS Edit before use 444 4E tAE 4E AE AE dE AE FE AE HE HE HE FE AE FE FE AE FE FE FE FE AE E FE FE FE AE FE FE AE FE FE FE FE FE FE FE E FE FE FE FE FE FE E E FE FE FE AE FE FE HE FE AE E TE HE FE E FE E H 1 Configure your server connection parameters SERVER localhost PORT 7777 USER root PASSWORD default 2 Configure the path to the CLC Server Command Line tools SERVERCMDPATH home user clcservercmdline clcserver PARSECMDPATH home user clcservercmdline clcresultparser 13 CHAPTER 3 EXAMPLE SCRIPT 14 3 Configure High throughput sequencing data import location for import data Use the server web interface to setup a data import location Copy the example files from the data directory to this location Edit the IMPORTPATH variable below to a CLC URL point to this location For more info please visit http www clcsupport com clcgenomicsserver current index php manual Accessing_files_on_writing_to areas_server_filesystem html For info
12. ons followed by an explanation of the basics of operating the CLC Server Command Line Tools Then we provide an example script which illustrates various aspects of how to use the analysis tools available on the server 1 1 Installation The CLC Server Command Line Tools can be downloaded from http www clcbio com products clc server command 1line tools direct download and is available for Windows Mac and Linux You can install the tools on any computer that can connect to your CLC Genomics Server but it makes sense to install them onto the computer that will be used to run the scripts or onto the server computer itself 1 2 System requirements The system requirements of CLC Server Command Line Tools are these 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 5 or later SUSE 10 or later e 32 or 64 bit e 256 MB RAM required e 512 MB RAM recommended e 1024 x 768 display recommended You will also need a running version of CLC Genomics Server No additional license is required for running the CLC Server Command Line Tools Chapter 2 Basic usage Once installed there will be three programs present in the installation folder e clcserver the key program It is used to run all the commands that communicate with the server e clcresultparser used to parse data locations from par
13. our system The file named as the parameter for the O option of the clcserver command is another example where you provide a location on your local file system 2 2 2 Data on the server For files already on the machine housing the CLC Genomics Server you need to provide the data location as a CLC URL These start with the text clc Files already uploaded to the CLC Genomics Server data area For files already available within the CLC Genomics Server you have a choice of providing a CLC URL with the human readable path to your file or providing a CLC URL with an ID that the CLC software understands The former is easier when working on the command line directly The latter is used primarily when working with pipelines of operations for example when scripting Examples of providing file locations for data uploaded to the CLC Genomics Server data area include e clc server server_data project1 samplel This refers to a file called sample1 on the server located in the server_data data location under the project 1 folder e clc server BAAAAAAPc132 7fff 268177574 7 f f This URL is also pointing to a file on the server using an ID to refer to it e clc server com 7777 server_data projectl samplel This is an example of using the server host name and port rather than just referring to server Since you need to be logged onto a CLC Genomics Server to get access to the data this form is generally not necessary The adv
14. rmation about CLC URLs please visit http www clcsupport com clcservercommandlinetools current index php manual Referring_files_CLC_URL html MPORTPATH clc serverfile tmp cmdline 4 Configure data paths for saving results Use the server web interface to configure a file system location for data storage Edit the DATAPATH variable below to a CLC URL pointing to this location For more info please visit http www clcsupport com clcgenomicsserver current index php manual Adding_file_system_location html For information about CLC URLs please visit http www clcsupport com clcservercommandlinetools current index php manual Referring_files_CLC_URL html DATAPATH clc server test DIR clc example SUBDIR workflow example FUNCTIONS AEE AE AE AE AE AE HE AE FE AE AE E FE FE AE AE AE FE FE FE AE AE AE FE FE FE AE AE E FE FE FE AE AE FE FE FE AE AE FE FE FE FE AE AE AE FE AE FE AE AE E FE FE AE AE AE FE FE FE AE AE AE FE FE FE AE AE AE FE FE AE AE AE FE FE FE AE AE AE FE E FE function check_return_code return_code cmdname 1 techo Return code return_code if return_code ne 0 then echo we echo Error during cmdname echo Terminating script exit 1 fi COMMANDS iat AEAEE at tat AE AE FE FE aE aE aE aE aE aE AE aE HE aE aE HE aE FE aE aE AE FE FE HE EEE aE EE HE EEE EEE aE EEE EEE EEE EEE EEE H SERVERCMD SSERVERCMDPATH S S SERVER P PORT U SUSER W SPASSWORD PARSECMD PARSECMDPA
15. sing which of these two clients the graphical or the command line to use for your work e For visualization and interpretation of data we recommend the CLC Genomics Workbench The only way to visualize and interpret data when you have worked using the CLC Server Command Line Tools is to export the results into file formats that can be imported into visualization tools e For explorative work we recommend using the CLC Genomics Workbench The numerous parameters are easier to interpret using the graphical interface and selection and man agement of data is more intuitive through this interface for most users In addition the graphical user interface has more constraints to help guide reasonable choices of parame ters and combination of parameters these constraints are not all present in the CLC Server Command Line Tools e For automation and consistency of particular utility in production environments the CLC Server Command Line Tools client is recommended In particular you can script pipelines of analyses on the CLC Genomics Server and then use these scripts for processing many data sets in a consistent manner For initial pilot runs it is often helpful to use the exploratory features of the CLC Genomics Workbench to determine quality control and parameter settings and then incorporate these settings into a script using the CLC Server Command Line Tools CHAPTER 1 INTRODUCTION 5 This user manual begins with installation instructi
16. ticular text files generated during clcserver runs This command is most useful when connecting analyses in a scripting pipeline See section 2 3 e clcserverkeystore a helper tool for enabling passwords to be handled securely see section 2 1 The clcserver program requires the following four flags which provide information about the connection to the server S lt hostname or IP address of the server gt P lt port the server runs on gt When omitted port 7777 is used which is the default for server installations U lt user name gt The username used to log onto the server W lt password or token gt See section 2 1 for how to avoid entering passwords in clear text If you run the cleserver command with the above parameters and nothing else then a list of all commands that can be run on the server will be returned For example clcserver S server com U bob W secret The commands to be run on the server are supplied with the flag A lt command to be executed on server gt If you supply the A flag with a program name but do not provide the required flags for that program then a listing of the flags for that program will be returned For example a command of a form like CHAPTER 2 BASIC USAGE 7 clcserver S server com U bob W secret A read_mapping would return the full list of parameters for the read_mapping function including the pos sible values and descriptions This information for e
17. tools e g drag and drop system copy or move commands etc This is because the indexing system used within the CLC Server File locations is very sensitive to unexpected changes i e non CLC actions We highly recommend that any Import Export directories you configure on your CLC Server are NOT within an area designated as a CLC Server File Location fa ta SY presentation E server_data H E Ilumina GA Pa 454 G E RNA seq 20 NC_000019 selection brain1 2 braink LE show Ctrl O braink N a E braink ES old Show H em ain2 Toolbox gt a 1 i ihe Cut Ctrl X v lt enter search term m Copy Ctrl C E Pate car B Alignments and Tri 4 Delete Delete Figure 2 1 Copying a data object in the workbench will put the CLC URL on the clipboard You can then paste the URL into your command in the terminal Ex 2 3 Result files and connecting analyses in pipelines For each run of clcserver text information is returned providing a summary of the steps taken and the locations in ID form of any files generated The file containing this information will by default be created in the current directory and will be called result txt You can use the 0 option for the clcserver command if you wish to specify an alternative file to be written to An example of the type of contents you will see in a typical result file is shown below In this case it is a file that was g
18. usage for all commands can be found at http www clcsupport com clcservercommandlinetools current index php manual Usage_all_commands h tml 16
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