CLCbio Genomics Workbench
Description
The CLCbio Genomics Workbench, for analyzing and visualizing next generation sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow. It enables everyone to rapidly analyze and visualize the huge amounts of data generated by NGS machines.
License
CLCbio Genomics Workbench version 9.5.3: module CLCgenomicsWB-9.5.3
- upgrade of a license purchased by Centre CERIT-SC (available for all the MetaVO users) allowing 2 simultaneous runs of the application
CLCbio Genomics Workbench version 7.0: module CLCgenomicsWB-7.0
- upgrade of a license purchased by Centre CERIT-SC (available for all the MetaVO users) allowing 2 simultaneous runs of the application
CLCbio Genomics Workbench version 6.5.1: module CLCgenomicsWB-6.5
- a license purchased by Centre CERIT-SC (available for all the MetaVO users) allowing 2 simultaneous runs of the application
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of CLCgenomics and load default version of CLCgenomics as
module avail CLCgenomics/ # list available modules module load CLCgenomics # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail CLCgenomics
and choose explicit version you want to use.
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Important: When requesting a job that will use the application, do not forget to ask the scheduler for starting the job when an application license is available, i.e., submit the job with e.g.
qsub -l nodes=1:ppn=X:... -l clcgenomics=1 when requesting a single license to be available. |
Load the appropriate module and run the CLCbio Genomics Workbench application. The application requires a graphical interface available.
$ module add CLCgenomicsWB-9.5.3
$ clcgenomicswb9
Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.
Documentation
Documentation is available on the official producer's webpage or locally in the program directory (/software/clcgenomicswb/v9.5.3/doc/, /software/clcgenomicswb/v7.0/doc/ or /software/clcgenomicswb/v6.5/doc/)