CLC Genomics Server
Contents
1. Contrary to processes running locally running server processes will appear even if you restart the Workbench and log into the server Server processes that are finished when you close the Workbench will not be shown when you start the Workbench again CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH mRNA Sequencing Building contigs 18 Set Up Experiment FF CENENE mRNA Sequencing Done SNP Detection number 2 in queue o m J J De Novo Assembly number 1 in queue o mJ O Reference Assembly Building contigs o mmnm jx Processes Toolbox Figure 2 9 Monitoring processes Chapter 3 Using a web browser as client Besides using the CLC Workbench as client you also have access to the server from the web interface The web interface gives you access to browsing and searching data and importing and exporting data Simply type the address of the server into your browser followed by the port number and you will see the login dialog see figure 3 1 you will need to get information from your server administrator about the server address z v e A El Ke A http servertest clcbio com 7777 J Gi Google 5 CLC Science Server Figure 3 1 The web interface of the server 3 1 Browsing and searching data To the left you will see the data locations connected to the server You can browse the folder hierarchy of the data location When you click an element2. Choose export format for aTP8a1 genomic sequence IOC ATP8a 1 genomic sequence Annotation Comma separated values csv FC ATP8a1 mRNA Choose where to save CATP8a1 genomic sequence SVWATP8a1 Download Save on server cloning Choose folder location for saving export E lPrimers 5 E limport export e m os 1 d rie test data Enter search term Folder test data was chosen as export location Choose where to execute the export Server Grid PCR Export Figure 3 4 Exporting sequences to the server 1 7
3. Sequencing data Salzberg S L Holt R A Kodira C D Lu F Chen L Deng Z t My folder Evangelista C C Gan W Heiman T J Li J Li Z Merkulov G V Milshina N V Naik A K Qi R Shue B C Wang A Wang J ILEATP8a1 alignment Wang X Yan X Ye J Yooseph S Zhao Q Zheng L Zhu S C Biddick K Bolanos R Delcher A L Dew I M Fasulo D R NC_000017 Genome Flanigan M J Huson D H Kravitz S A Miller J R Mobarry C M Reinert K Remington K A Zhang Q Zheng X H Nusskern D R tutorial data x Lai Z Lei Y Zhong W Yao A Guan P Ji R R Gu Z 4 m i Wang Z Y Zhong F Xiao C Chiang C C Yandell M Wortman J R Amanatides P G Hladun S L Pratts E C Johnson J E Dodson K L Woodford K J Evans C A Gropman B Enter search term a Rusch D B Venter E Wang M Smith T J Houck J T ba Tommkina D R Haunea Tarnh D Chin S H Allen D R 4 fil p Figure 3 2 Inspecting the text view of a protein sequence Note that these views are a subset of the views that you find in the CLC Workbench 3 2 Import and export It is possible to import from and export to the server If you wish to import data from the server click Import E and select the relevant data Leave the file import format to Automatic and press the Import File button Figure 3 3 You can also put data into the import export directories Select the data you wish to export and click Expor
4. SxS CLC Genomics Server End User USER MANUAL Manual for CLC Genomics Server 6 0 Windows Mac OS X and Linux February 7 2014 This software is for research purposes only CLC bio a QIAGEN Company Silkeborgvej 2 Prismet DK 8000 Aarhus C Denmark CC big A QIAGEN Company Contents 1 Introduction 2 Using the server from a CLC Workbench 2 1 Installing relevant plugins in the Workbench 2 000405 ee 2 2 Log nto the Sever cw es we oe ee ew ee ewe Ew oe we ee Ee 2 3 Browsing and searching data from the workbench 23 4 Deleng Cale as Si as ir ani ant bea 2 4 Running analyses on the server ee 0 2 5 Accessing files on and writing to areas of the server filesystem 2 6 Monitoring processes a e a a a ee 3 Using a web browser as client 3 14 Browsing and searching data s s s s a been eee ee ko Bowe eo ee ee ae Irom ie OOE ae ea ee eR eee ea eee hee ee eee OO 00 10 10 11 13 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 The basic idea is that you can have the Server store data and run jobs centrally and thereby offload personal and typically smaller computers For the user the difference between working just with a Workbench and working with a Workbench and a server is very small All the mechanisms for managing data u
5. in the tree a number of options are available e Click the Element Info tab to see the properties of this element Note that you can edit the information in this view e Click the History Li tab to see the history of this element 15 CHAPTER 3 USING A WEB BROWSER AS CLIENT 16 e Click the Sequence Text tab to see a textual representation of this element only works for Sequences An example of a protein sequence in the text view is shown in figure 3 2 report a bug check setup logout root g CLC Genomics Server Beta Ecc Data CA History AASA gt Export data F8 Import data STA Admin W JeExample Data FC ATP8a 1 genomic sequence i LOCUS ATP8al genomic sequence 228194 bp DNA linear CON 20 JUN 2007 XS ATP8a1 mRNA DEFINITION Mus musculus chromosome 5 genomic contig alternate assembly based on Celera assembly Matpgai ACCESSION NW_001030787 E VERSION NW_001030787 1 GI 82897198 Cloning KEYWORDS kB SOURCE Mus musculus house mouse ORGANISM Mus musculus CaiProtein analyses Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Eutheria Euarchontoglires Glires Rodentia Lai protein orthologs Sciurognathi Muroidea Muridae Murinae Mus C OREFERENCE 1 bases 1 to 61163717 URNA secondary structure AUTHORS Mural R J Adams M D Myers E W Smith H O Miklos G_L f Wides R Halpern A Li P W Sutton G G Nadeau J
6. al to running the same analyses in the Workbench with three exceptions e You can only select data from the data locations connected to the server This means that the Navigation Area is filtered to only show these locations e You have to save the result In the last step you can normally choose between Open and Save but for the analyses performed on the server you have to choose Save e When you click Finish the analysis is performed on the server This means that you can close the Workbench or disconnect the computer from the server and the analysis will CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 11 r g Map Reads to Reference 1 Choose where to run a BO LR Remember setting and skip this step Figure 2 4 Selecting where to run the analysis continue to run When you log in after the analysis is done you will get a notification in the Workbench Note that when using the import tool Figure 2 5 for importing high throughput sequencing data on the server only for Genomics Workbench and Server the first part of the import is uploading the data to the server and during this part the Workbench has to maintain connection to the server If you try to close the Workbench during upload you will get a warning dialog The upload runs as a local process in Processes tab in the lower left corner and when the upload is done a new process is started that has a server icon and runs on the serve
7. cted Elements 1 2 Choose import files i location LS locations 127 0 0 1 500 csfasta E ga import export 3 Import files and options 5 2 test data 3 solid paired 9 single _ 500_QV qual E ref for 500 fa solidfastq single huma S solidTests txt p General options Paired reads Paired read information 4 Discard read names 4 Discard quality scores Figure 2 8 Selecting files on server file system Note Import Export locations should NOT be set to subfolders of any defined CLC file or data location CLC file and data locations should be used for CLC data and data should only be added or removed from these areas by CLC tools By definition an Import Export folder is meant for holding non CLC data for example sequencing data that will be imported data that you export from the Genomics Server or blast databases Note that your server administrator needs to configure the server to import files directly from the server file system 2 6 Monitoring processes Just as for processes running locally you will be able to monitor processes running on the server Click the Processes tab next to the Toolbox and you will see the list of processes see figure 2 9 Note that the processes running on the server have a server icon ls or 5 whereas the processes running locally have specific icons like 2 and Fan You can also see that two of the server processes are queued
8. eads Compare Variants GO Enrichment Analysis Functional Consequences Amino Acid Changes Functional Consequences Annotate with Conservation Score Functional Consequences Predict Splice Site Effect Functional Consequences e Transcriptomics Analysis Expression Analysis RNA Seq Analysis Extract and Count Small RNA Analysis Annotate and Merge Counts Small RNA Analysis Create Histogram General Plots e Epigenomics Analysis ChiP Seq Analysis e De Novo Sequencing De Novo Assembly Map Reads to Contigs The functionality of the CLC Genomics Server can be extended by installation of Server plugins The available plugins can be found at http www clcbio com server_plugins Chapter 2 Using the server from a CLC Workbench 2 1 Installing relevant plugins in the Workbench In order to use the CLC Genomics Server from a CLC Workbench you need to install the CLC Workbench Client Plugin in the Workbench This will allow you to log into the CLC Server access data from the CLC Server data locations and submit analyses to your CLC Server Plugins are installed using the Plugins and Resources Manager which can be accessed via the menu in the Workbench Help Plugins and Resources or via the Plugins 3 button on the Toolbar From within the Plugins and Resources Manager choose the Download Plugins tab and click on the CLC Workbench Client Plugin Then click in the button labe
9. g into the server when the Workbench starts Note that you need to get the login information from your server administrator When you press Login the Workbench connects to the server You will see a progress bar in the login dialog If the login is successful the dialog will disappear and you will be able to use the server as described below 2 3 Browsing and searching data from the workbench Once you are logged in the data locations on the server are shown in the Navigation Area Figure 2 3 Once logged in the server data locations can be used in the same way as local data locations We refer to the users manual of the Workbench for information about using the Navigation Area click the location and press Fi on the keyboard to get context help You may also wish to have a look at the search chapter Searching your data in the workbench user manual press FT and look for Searching your data It is possible to have both local and server locations added at the same time This means that you can work on e g temporary sequences located on your own computer and then when you have more complete results you can drag the elements to a folder in the server location CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 10 2 nobackup ja CLC_Data MySql cledb storage office He Oracle orcl storage office ca Presentation g test q training Ca tutorials H H H H H OR 2 2 Figure 2 3 Three server loca
10. in the Workbench for certain activities e g importing data functions The import export directories can be accessed from the Workbench via the Import function in the Workbench If a user that is logged into the CLC Genomics Server via their CLC Workbench wishes to import e g high throughput sequencing data an the option shown in figure 2 7 will appear E souio 1 Choose where to run Serpa Bool ad 2 Choose import files location Where are your files located On my local disk or a place I have access to On the server or a place that the server has access to A Previous gt Next Finis X Cancel Figure 2 7 Deciding source for high throughput sequencing data files CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 13 On my local disk or a place have access to means that the user will be able to select files from the file system of the machine their CLC Workbench is installed on These files will then be transferred over the network to the server and placed as temporary files for importing If the user chooses instead the option On the server or a place the server has access to the user is presented with a file browser for the selected parts of the server file system that the administator has configured as an Import export location Figure 2 8 5 E souio 0 SOLID 1 Choose where to run i RL SIS EAU bi LES AL ELA semen Server Files Sele
11. inistrator s point of view this is about configuring folders that are safe for the CLC Genomics Server to read and write to on the server machine system This means that users logged into the CLC Genomics Server from their Workbench will be able to access files in that area and potentially write files to that area Note that the CLC Genomics Server will be accessing the file system as the user running the server process not as the user logged into the Workbench This means that you should be careful when opening access to the server filesystem in this way Thus only folders that do not contain sensitive information should be added Folders to be added for this type of access are configured in the web administration interface Admin tab Under Main configuration open the Import export directories Figure 2 6 to list and or add directories Element Info C History Sequence Text SExportdata Import data J Admin 59 Main configuration D Database locations D File system locations h Import export directories Add new import export directory Remove Path C server import export configuration D HTTP settings Save Configuration Figure 2 6 Defining source folders that should be available for browsing from the Workbench Press the Add new import export directory button to specify a path to a folder on the server This folder and all its subfolders will then be available for browsing
12. led Download and Install If you are working on a system not connected to the network then you can also install the plugin by downloading the cpa file from the plugins page of our website abt Wwww C1l e156 con clae plicin Then start up the Plugin manager within the Workbench and click on the button at the bottom of the Plugin manager labeled Install from File You need to restart the Workbench before the plugin is ready for use 2 2 Log into the server Once the plug in is installed log into the server File CLC Server Login E That will bring up a login dialog as shown in figure 2 1 The first time you log into the server you have to expand the dialog by clicking Advanced That will allow you to enter the host and port for the server as shown in figure 2 2 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 2 USING THE SERVER FROM A CLC WORKBENCH 9 amp CLC Server Login User name testuser H Advanced Figure 2 1 Expand the login dialog by clicking Advanced CLC Server Login User name testuser Advanced Server host hostname Server port 7777 Save user name and password Automatic login Figure 2 2 Specifying host and port In addition you can choose to save user name and password and automatically lo
13. nage BLAST Databases e NGS Core Tools Create Sequencing QC Report Merge Overlapping Pairs Trim Sequences Map Reads to Reference Local Realignment Create Detailed Mapping Report Merge Read Mappings Extract Consensus Sequence Process Tagged Sequences Multiplexing e Track Tools Convert to Tracks Convert from Tracks Merge Annotation Tracks Annotate with Overlap Information Annotate and Filter Extract Reads Based on Overlap Annotate and Filter Filter Annotations on Name Annotate and Filter Filter Based on Overlap Annotate and Filter Create GC Content Graph Tracks Graphs Create Mapping Graph Tracks Graphs Identify Graph Threshold Areas Graphs e Resequencing Analysis Create Statistics for Target Regions Probabilistic Variant Detection Quality based Variant Detection InDels and Structural Variants Coverage Analysis Annotate from Known Variants Annotate and Filter Variants Filter against Known Variants Annotate and Filter Variants Annotate with Exon Numbers Annotate and Filter Variants Annotate with Flanking Sequences Annotate and Filter Variants Filter Marginal Variant Calls Annotate and Filter Variants CHAPTER 1 INTRODUCTION Filter Reference Variants Annotate and Filter Variants Compare Sample Variant Tracks Compare Variants Compare Variants within Group Compare Variants Fisher Exact Test Compare Variants Trio Analysis Compare Variants Filter against Control R
14. r View Download Toolbox Workspace Help Lil ce b w Seve import Export Graphic Print Undo Redo BUON Area Ee Standard Import Ctrl I Ha S ay 1S kar Tracks Data Roche 454 LE Illumina 206 ATP amp C SOLID Ss ATP3 T CS Clonir Hee Fasta E Prime Sanger tai Prote 5 es Ion Torrent tal Prote C RNAs SAM BAM Mapping Files Figure 2 5 The import tool in the Workbench If you need help on the analyses themselves please click the Help button in the dialog That will take you to the relevant part of the user manual of the Workbench 2 5 Accessing files on and writing to areas of the server filesystem There are circumstances when it is beneficial to be able to interact with non CLC files directly on your server filesystem A common circumstance would be importing high throughput sequencing data from folders where it is stored on the same system that your CLC Genomics Server is running on This could eliminate the need for each user to copy large sequence data files to the machine their CLC Workbench is running on before importing the data into a CLC Genomics Server CLC server data area Another example is if you wish to export data from CLC format to other formats and save those files on your server machine s filesystem as opposed to saving the files in the system your Workbench is running on CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 12 From the adm
15. sing the tools and visualizing the data are the same This user manual is intended to show how to take advantage of the server as a user For information about administrating the server please see the Administrator Manual The CLC Genomics Server is shipped with the following tools and analyses that can be started from the CLC Genomics Workbench or CLC Server Command Line Tools e Import Export Download Genome Alignments and Trees Create Alignment Create Tree Maximum Likelihood Phylogeny General Sequence Analysis Extract Annotations Extract Sequences e Nucleotide Analysis Translate to Protein Convert DNA to RNA Convert RNA to DNA Reverse Complement Sequence CHAPTER 1 INTRODUCTION Clients CLC Genomics g Custom Workbench client i oe Scalability WOIJEZIWOYSN t i ae i B Bioinformatics Custom designed 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 Reverse Sequence Find Open Reading Frames e Sequencing Data Analysis Trim Sequences Assemble Sequences Assemble Sequences to Reference Secondary Peak Calling e Primers and Probes Find Binding Sites and Create Fragments e BLAST CHAPTER 1 INTRODUCTION BLAST BLAST at NCBI Download BLAST Databases Create BLAST Database Ma
16. t ES Next tick Save on server and select the folder where you want the data to be see figure 3 4 Click the button labeled Export The server will automatically recognize the file format and interpret the file CHAPTER 3 USING A WEB BROWSER AS CLIENT report a bug check setup logout root CLC Genomics Server Beta gcc pata Y ElementInfo Q History E Sequence Text Import data example Data _ Choose a file to be uploaded into IRNA secondary structure items Select a local file or a server file to import C Import local file XC ATP8a1 mRNA sport server Be SMATP8a1 Flimport export cloning test data primers solid lprotein analyses 8 amp paired Ciprotein orthologs C matepairref 16 intact pairs distance 180 to 25000 fa RNA secondary structure Cireference fa CalSequencing data at solid paired end_F3 csfasta J mt a eeno gi is solid paired end_F3 qual e solid paired end_F5 8C csfasta Enter search term fe solid paired end_F5 BC qual D solid paired end_F5 P2 csfasta File _ reference fa has been chosen for import Select file import format Automatic T Choose where to execute the import Server Grid Import File Figure 3 3 Importing a sequence from the server report a bug check setup logout root g CLC Genomics Server Beta GICLC_Data Sequence Text ANT iA Admin ElExample Data
17. tions on the server appears in the Navigation Area marked with blue dots The remaining five local folders are file locations in the Workbench that are independent of the server 2 3 1 Deleting data When you delete data located on the server it will be placed in the Recycle bin ff in the same way as when you delete data located on the Workbench The data in the recycle bin can only be accessed by you and the server administrator Please note that the server administrator might have configured the recycle bin to be automatically emptied at regular intervals 2 4 Running analyses on the server The tools available on the server are listed in the introduction see section 1 For more information on the tools please see the manual for CLC Genomics Workbench at http www clcbio com usermanuals or click the Help button in the dialogs that are shown when you run the tools When you run the analyses you will be faced with an initial dialog with two choices e Workbench This will run the analysis on your computer e Server This will run the analysis on the server An example of such a dialog is shown in figure 2 4 Note that you can check the Remember setting and skip this step option to always use the selected option when the analysis dialog is shown If you change your mind later on and want to switch simply click Previous in the dialog and you will be able to change the setting Running the analyses on the server is identic
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