CLC Server - CLC Manuals
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1. Assemble Sequences to Reference Sequencing Data Analysis Secondary Peak Calling Sequencing Data Analysis Find Binding Sites and Create Fragments Primers and Probes Epigenomics Analysis Transcription Factor ChIP Seq Annotate with Nearby Gene Information Legacy Tools Probabilistic Variant Detection Legacy Quality based Variant Detection Legacy The functionality of the CLC Server can be extended by installation of Server plugins The available plugins can be found athttp www clcbio com server plugins2. CLC Server End User USER MANUAL Manual for CLC Server 7 5 1 Windows Mac OS X and Linux November 12 2015 This software is for research purposes only CLC bio a QIAGEN Company Silkeborgvej 2 Prismet DK 8000 Aarhus C Denmark LU bio A QIAGEN company Contents 1 Introduction 2 Using the server from a CLC Workbench 2 1 Installing relevant plugins in the Workbench 2 005005 ee 2 4 Log nto the Sever cw es we oe Ea ew di ee Ew oe we ee E E a 2 3 Browsing and searching data from the workbench 206 Poa PEC CM as i ge arp keew aed eee head oe tee ee be a 2 4 Running analyses onthe server 1 ee ee 2 5 Accessing files on and writing to areas of the server filesystem 2 6 Monitoring processes a noaoo ee ee 3 Using a web browser as client 3 14 Browsing and searching data s s s s a been eee ee ELES LEENE E Se MHN ie EO o ae eae eRe ee ea eo ee ee ee DE 4 Appendix 4 1 CLC Genomics Server 00 2 ee ee ee ee ee a 4 2 Biomedical Genomics Server Extension 0 0 0 8 ee eee ee es o oOo N O0 O Q Chapter 1 Introduction Welcome to CLC Server 7 5 1 a central element of the CLC product line enterprise solutions The latest version of the user manual can also be found in pdf format at http www clcbio com usermanuals You can get an overview of the server solution in figure 1 1 The software depicted here including CLC Server is for re
3. CLC Server Command Line Tools e Import Export e Download Reference Genome Data Classical Sequence Analysis Create Alignment Alignments and Trees K mer Based Tree Construction Alignments and Trees Create Tree Alignments and Trees Model Testing Alignments and Trees Maximum Likelihood Phylogeny Alignments and Trees Extract Annotations General Sequence Analysis Extract Sequences General Sequence Analysis Motif Search General Sequence Analysis Translate to Protein Nucleotide Analysis Convert DNA to RNA Nucleotide Analysis Convert RNA to DNA Nucleotide Analysis Reverse Complement Sequence Nucleotide Analysis Reverse Sequence Nucleotide Analysis Find Open Reading Frames Nucleotide Analysis Download Pfam Database Protein Analysis Pfam Domain Search Protein Analysis e Molecular Biology Tools 1 7 CHAPTER 4 APPENDIX Assemble Sequences Sequencing Data Analysis Assemble Sequences to Reference Sequencing Data Analysis Secondary Peak Calling Sequencing Data Analysis Find Binding Sites and Create Fragments Primers and Probes Add attB Sites Cloning and Restriction Sites Gateway Cloning Create Entry clone BP Cloning and Restriction Sites Gateway Cloning Create Expression clone LR Cloning and Restriction Sites Gateway Cloning e BLAST BLAST BLAST at NCBI Download BLAST Databases Create BLAST Dat
4. Hapmap From Databases Add Information to Genes Add Information from Overlapping Variants Compare Samples Compare Shared Variants Within a Group of Samples identify Enriched Variants in Case vs Control Group Trio Analysis Identify Candidate Variants Identify Candidate Variants Remove Information from Variants Identify Variants with Effect on Splicing Identify Candidate Genes Identify Differentially Expressed Gene Groups and Pathways Identify Highly Mutated Gene Groups and Pathways Identify Mutated Genes Select Genes by Name Expression Analysis Extract Differentially Expressed Genes RNA Seq Analysis RNA Seg Analysis Create Fold Change Track RNA Seq Analysis Extract and Count Small RNA Analysis Annotate and Merge Counts Small RNA Analysis Create Box Plot Quality Control Hierarchical Clustering of Samples Quality Control Principal Component Analysis Quality Control Empirical Analysis of DGE Statistical Analysis Proportion based Statistical Analysis Statistical Analysis CHAPTER 4 APPENDIX 23 Gaussian Statistical Analysis Statistical Analysis Create Histogram General Plots e Helper Tools Extract Sequences Filter Based on Overlap e Cloning and Restriction Sites Add attB Sites Gateway Cloning Create Entry clone BP Gateway Cloning Create Expression clone LR Gateway Cloning Sanger Sequencing Assemble Sequences Sequencing Data Analysis
5. PSS JJOO I ASIYE TEAS TG SVOU COMO ICU TAT AU TEUS lida Server Files Selected Elements 1 2 Choose import files z zer E heroine gt locations 127 0 0 1 500 csfasta import export 3 Import files and options C gt test data solid paired g single 500 csfasta 500 QV qual E ref for 500 fa solidfasta single humal solidTests txt mW j General options Paired reads Paired read information V Discard read names Mate pair R3 F3 Paired end F3 F5 Discard quality scores Minimum distance 180 Maximum distance 250 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 CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 12 from the CLC 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 You can monitor processes running on the server or the local Workbench by opening the Processes tab at the bottom left of the Workbench This tab is next to
6. files on your server machine s filesystem as opposed to saving the files in the system your Workbench is running on From the administrator s point of view this is about configuring folders that are safe for the CLC Server to read and write to on the server machine system This means that users logged into the CLC Server from their Workbench will be able to access files in that area and potentially write files to that area Note that the CLC 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 5 Element Info LE History Sequence Text Export data 4 Import data d Admin 13 Main configuration P Database locations File system locations Y import export directories Add new import export directory Remove Path C server import export confiueaion P 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
7. Automatic h Choose where to execute the import 9 Server Grid Import File Figure 3 3 Importing a sequence from the server report a bug check setup logout root DDS CLC Drug Discovery Server localhost Version 1 0 Beta FS molecule library gt Molecule library mol2 The file will be uploaded into CLCServerData gt AllDecoysOrdered mol2 Select file to import _ Import local file gt egfr_decoys mol2 5 e Import server file gt 32000_compounds mol2 os J cicServerData Import molecules from SMI E inve ligand clc EB nvr ligand 3 E IHR target docking results clc 1HVR target E 1HvVR target screening results clc ESinve target docking resul E iHVR_target cle Dock Ligands Pipelined lo n 32000_compounds mol2 E 1HVR target screening res n gt AllDecoysOrdered mol2 o File T AllDecoysOrdered mol2 has been chosen for import Select file import format Enter search term Automatic Choose where to execute the import Server Grid Import File lt bio Figure 3 4 Importing molecules from the server 15 CHAPTER 3 USING A WEB BROWSER AS CLIENT 16 report a bug check setup logout root g CLC Genomics Server Beta CRICLC Data Sequence Text PASCALE lExample Data Choose export format for 2 ATP8a 1 genomic sequence XX ATP8a 1 genomic sequence Annotation Comma separated values csv x AX ATP8a1 mRNA Choose where to save ATP8a1 genomic sequence Mat
8. 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 hast 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 log 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 user 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 F1 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 co
9. abase e NGS Core Tools Sample Reads Create Sequencing QC Report Merge Overlapping Pairs Trim Sequences Demultiplex Reads Map Reads to Reference Local Realignment Create Detailed Mapping Report Merge Read Mappings Remove Duplicate Mapped Reads Extract Consensus Sequence 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 CHAPTER 4 APPENDIX 19 Create Statistics for Target Regions InDels and Structural Variants Coverage Analysis Basic Variant Detection Variant Detectors Fixed Ploidy Variant Detection Variant Detectors Low Frequency Variant Detection Variant Detectors 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 Filter Reference Variants Annotate and Filter Variants Compare Sample Variant Tracks Com
10. in the dialogs that are shown when you run the tools When you run the analyses you will be faced with an initial dialog asking you where you wish the analysis to be run e Workbench Run the analysis on the computer the CLC Workbench is running on e Server Run the analysis using the CLC Server For job node setups analyses will be run on the job nodes e Grid Submit the job to the CLC Server such that the job is then sent to be run on grid nodes An example of such a dialog is shown in figure 2 4 You can check the Remember setting and skip this step option if you wish to always use the selected option when submitting analyses If you change your mind later on and want to switch click Previous in the dialog when you start up an analysis You will then be taken back to the dialog where you can choose where the analysis should be run CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 9 r E Map Reads to Reference 1 Choose where to run a DS cab OE becceseeseceeseseoeocsessod Remember setting and skip this step Figure 2 4 Selecting where to run the analysis Launching an analyses to run on a CLC Server or on grid nodes is identical to launching the same analyses to run on a Workbench but there are three things to be aware of e You can only select data stored in locations configured on the server with the exception of running data import This means that when
11. m the local system to the server system During the upload phase the Workbench must maintain its connection to the server If you try to close the Workbench during this phase you will see a warning dialog You can see what stage tasks are at by opening the Processes tab in the lower left corner of the Workbench Data upload from the Workbench to the server runs as a local process in the Processes tab When the upload is done a new process for the import is started This will have a server icon At this point you can disconnect or close your Workbench without affecting the import CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 10 File Edit View Download Toolbox Workspa CE ss Show New Seve import Export Graphics Print Navigation rea Figure 2 5 Import tools are found under this menu in the Workbench 2 5 Accessing files on and writing to areas of the server filesystem There are situations when it is beneficial to be able to interact with non CLC files directly on your server filesystem A common use case would be importing high throughput sequencing data or large molecule lioraries from folders where it is stored on the same system that your CLC Server is running on This could eliminate the need for each user to copy large data files to the machine the CLC Workbench is running on before importing the data into a CLC Server data area Another example is if you wish to export data from CLC format to other formats and save those
12. mputer 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 8 2 nobackup ja CLC Data MySql cledb storage office DO Oracle orcl storage office Ca Presentation g test ia training Ha tutorials H H H H H O O Figure 2 3 Three server locations 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 Note that when logged in a CLC Server with a Biomedical Genomics Server Extension you will have in your Navigation Area two folders called CLC_References The blue dot indicates which of these repositories is installed on 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 different types of CLC Server are listed in section 4 1 and section 4 2 For more information on the tools please see the manual for the workbench at http www clcbio com usermanuals or Click the Help button
13. ngs Copy Number Variant Detection Remove Duplicate Mapped Reads Indels and Structural Variants Whole Genome Coverage Analysis Basic Variant Detection Variant Detectors Fixed Ploidy Variant Detection Variant Detectors Low Frequency Variant Detection Variant Detectors e Add Information to Variants Add Information from Variant Databases Add Conservation Scores Add Exon Number Add Flanking Sequence Add Fold Changes Add information about Amino Acids Changes Add Information from Genomic Regions Add Information from Overlapping Genes Link Variants to 3D Protein Structure Download 3D Protein Structure Database Add Information from 1000 Genomes Project From Databases Add Information from COSMIC From Databases Add Information from Clinvar From Databases Add Information from Common dbSNP From Databases Add Information from Hapmap From Databases Add Information from dbSNP From Databases e Remove Variants Remove Variants Found in External Databases Remove Variants Not Found in External Databases 21 CHAPTER 4 APPENDIX 22 Remove False Positive Remove Germline Variants Remove Reference Variants Remove Variants Inside Genome Regions Remove Variants Outside Genome Regions Remove Variants Outside Targeted Regions Remove Variants Found in 1000 Genomes Project From Databases Remove Variants Found in Common dbSNP From Databases Remove Variants Found in
14. on the server This folder and all its subfolders will then be available for browsing in the Workbench for certain activities e g importing data functions CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 11 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 Server via their CLC Workbench wishes to import e g high throughput sequencing data an option like the one shown in figure 2 7 will appear r E souio 1 Choose where to run Mes odan 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 Figure 2 7 Deciding source for e g high throughput sequencing data files 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 an example is shown in figure 2 8 E so 1 Choose where to run o SLL THES UI
15. orkbench 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 4 and select the relevant data Leave the file import format to Automatic and press the Import File button Figure 3 3 and Figure 3 4 You can also put data into the import export directories Select the data you wish to export and click Export Next tick Save on server and select the folder where you want the data to be see figure 3 5 and figure 3 6 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 g CLC Genomics Server Beta Ecc Data Example Data _ Choose a file to be uploaded into RNA secondary structure XX ATP8a1 genomic sequence SS ads or pa mio Import local file AX ATP8a1 mRNA ieee Matpsai Elimport export 2 icloning test data primers Elsolid protein analyses O Elpaired E protein orthologs Imatepairref 16 intact pairs distance 180 to 25000 fa Erna secondary structure P sequencing data al solid paired end_F3 csfasta P m Beat M solid paired end_F3 qual bd solid paired end F5 BC csfasta Enter search term i solid paired end_F5 BC qual D solid paired end_F5 P2 csfasta File Meee fa has been chosen for import Select file import format
16. pare Variants Compare Variants within Group Compare Variants Fisher Exact Test Compare Variants Trio Analysis Compare Variants Filter against Control Reads Compare Variants GO Enrichment Analysis Functional Consequences Amino Acid Changes Functional Consequences Annotate with Conservation Score Functional Consequences Predict Splice Site Effect Functional Consequences Link Variants to 3D Protein Structure Functional Consequences Download 3D Protein Structure Database Functional Consequences e Transcriptomics Analysis Expression Analysis Create Track from Experiment RNA Seq Analysis RNA Seg Analysis Extract and Count Small RNA Analysis Annotate and Merge Counts Small RNA Analysis Create Box Plot Quality Control Hierarchical Clustering of Samples Quality Control Principal Component Analysis Quality Control Empirical Analysis of DGE Statistical Analysis Proportion based Statistical Analysis Statistical Analysis Gaussian Statistical Analysis Statistical Analysis Create Histogram General Plots e Epigenomics Analysis Transcription Factor ChIP Seq CHAPTER 4 APPENDIX 20 Annotate with Nearby Gene Information e De Novo Sequencing De Novo Assembly Map Reads to Contigs e Legacy Tools Probabilistic Variant Detection Legacy Quality based Variant Detection Legacy ChIP Seq Analysis Legacy The functionality of the CLC Genomics Server can be extended by ins
17. psai Download o Ba 9 Save on server Cloning Choose folder location for saving export Primers a import export mia Ea e 4 T T oltest data E Te ea e A Folder l test data was chosen as export location Choose where to execute the export 9 Server Grid Figure 3 5 Exporting sequences to the server report a bug check setup logout root DDS CLC Drug Discovery Server localhost Version 1 0 Beta ES Molecule library 3 Import data 413 Admin T Molecule library mol2 Choose export format for E Molecule library CLC clc AllDecoysOrdered mol2 egfr_decoys mol2 Choose how to handle the export 32000_compounds mol2 Download Import molecules from SMI Save on server EHR ligand Choose folder location for saving export O IHR target LleLCServerData FS 1HVR target docking resul E AHVR_ligand cle Dock Ligands Pipelined lo E IHR target docking results clc EiHYR target screening res j E 1HVR target screening results clc Screen Liaands Pipelined iHVR_target cle T 32000 compounds mol2 allDecoysOrdered mol2 Folder CLCServerData was chosen as export location Enter search term Choose where to execute the export e Server Grid Export tt bio Figure 3 6 Exporting molecules to the server Chapter 4 Appendix 4 1 CLC Genomics Server The CLC Genomics Server is shipped with the following tools and analyses that can all be started from CLC Genomics Workbench and
18. rver administrator about the server address lt v Cc A F A kg TRE http servertest clcbio com 7777 LS IG 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 element in the tree a number of options are available e Click the Element Info 5 tab to see the properties of this element Note that you can edit the information in this view e Click the History tab to see the history of this element 13 CHAPTER 3 USING A WEB BROWSER AS CLIENT 14 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 Fa Data LE History Ee Pega ro a Export data C Import data STA Admin Example Data F XC ATP8a1 genomic sequence i LOCUS ATP8al genomic sequence 228194 bp DNA linear CON 20 JUN 2007 XX 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 a SOURCE Mus musculus house mouse ORGANISM Mus musculus H Protein analyse
19. s Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi o Mammalia Eutheria Euarchontoglires Glires Rodentia E Protein orthologs Sciurognathi Muroidea Muridae Murinae Mus OREFERENCE 1 bases 1 to 61163717 RNA 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 Sequencing data Salzberg S L Holt R A Kodira C D Lu F Chen L Deng Z a 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 iEEATP8al 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 A Reinert K Remington K A Zhang Q Zheng X H Nusskern D R tutorial data 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 Tommkina D R Havunea Jarnh D Chin S H Allen D R 4 44 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 W
20. search purposes only Using a server means that data can be stored centrally and analyses run on a central machine rather than a personal computer Please see Chapter 4 for a listing of tools shipped with CLC servers After logging into the CLC Server from a Workbench data on the server will be listed in the Workbench navigation area and analyses can be started as usual The key difference is that when you are logged into a CLC Server from a Workbench you will be get the choice of where to run the analysis on the Workbench or on the CLC Server This manual describes how to use a CLC Server as a Workbench user For information about administrating the server please see the Administrator Manual CHAPTER 1 INTRODUCTION Clients oem DA CLC workbench Browser UOI eZIWO SN 8 0 amp o Job Nodes Scalability External App DRMAA 2 oe aq 0 Bioinformatics Custom designed Database database schemas Data Management Figure 1 1 An overview of the server solution from CLC bio Note that not all features are included with all license models Chapter 2 Using the server from a CLC Workbench 2 1 Installing relevant plugins in the Workbench In order to use the CLC 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 s
21. tallation of Server plugins The available plugins can be found at http www clcbio com server plugins Latest improvements CLC Genomics Server is under constant development and improvement A detailed list that includes a description of new features improvements bugfixes and changes for the current version of CLC Genomics Server can be found at http www clcbio com products clc genomics server latest improvements 4 2 Biomedical Genomics Server Extension The Biomedical Genomics Server Extension can run all the tools and analyses available from both Biomedical Genomics Workbench and CLC Genomics Workbench as well as the pre installed workflows from Biomedical Genomics Workbench Here is the list of the tools of the Biomedical Genomics Workbench that can be started from Biomedical Genomics Workbench and CLC Server Command Line Tools e Import e Export e Download Reference Genome Data e Genome Browser Create GC Content Graph Graphs Create Mapping Graph Graphs Identify Graph Threshold Area Graphs Quality Control QC for Sequencing Reads QC for Target Sequencing QC for Read Mapping Preparing Raw Data CHAPTER 4 APPENDIX Merge Overlapping Pairs Trim Sequences Demultiplex reads e Resequencing Analysis Identify Known Mutations from Sample Mappings Trim Primers of Mapped Reads Extract Reads Based on Overlap Map Reads to Reference Local Realignment Merge Read Mappi
22. the Toolbox tab A list of submitted and running processes see figure 2 9 will be visible there PIMA Sequencing Building contigs TT 18 5 Set Up Experiment Ex NENENRANNRANNAANANANA 100 MRA Sequencing Done 2S PRR RR RRR R RRR RRRREEE ic0o SNP Detection number 2 in queue OL mm JJ De Novo assembly number 1 in queue OL Mm jz Reference Assembly Building contigs sI Processes Toolbox Figure 2 9 Monitoring processes Processes running on the server will have a server icon 8 whereas processes running locally have icons specific to the analysis being run for example 2 and In the image you can also see that two of the server processes are queued Server processes that are queued or running will reappear in the Workbench processes tab if you restart the Workbench and log into the server Server processes that are finished when you close the Workbench will not be shown again in the processes tab when you restart your Workbench Chapter 3 Using a web browser as client Besides using the CLC Workbench as a 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 a login dialog similar to what is shown in figure 3 1 you will need to get information from your se
23. ubmit 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 2 or via the Plugins 4 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 on the button labeled Download and Install If you are working on a system not connected to the internet then you can also install the plugin by downloading the cpa file from the plugins page of our website atip www Clco10 com cle pluginy 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 plugin 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 plugins 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 f amp CLC
24. you are given the option to choose the data to use in an analysis only server locations are shown Further information about the exceptional case of data import is provided below e You have to save the result For single analyses run on the Workbench you can normally choose how to handle the results Open or Save Results from analyses performed on the server must be saved so the option to open the results instead of saving them will be unavailable e When you click Finish the analysis is submitted to the server to be handled This means that you can close the Workbench or disconnect from the server without affecting the analysis See the notes on import below for an exception to this If an analysis has been completed when your Workbench is closed or while it is not connected to the server you will see a notification about this when you next log into the server from the Workbench Important note about data import to a server from a Workbench When using an import tool Figure 2 5 you are offered the option of importing data from a local area that is an area accessible from the machine the CLC Workbench is running on or from an area the CLC Server has access to When importing data into the server from an area the CLC Server has access to you can close your Workbench or disconnect it right after submitting the job However when importing data from your local system to a server the first part of the import involves uploading the data fro
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