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Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

Binary install of Complete Genomics Analysis Tools


1.7.1 (2013-08-29)

 # binary download
 cd /share/apps/ngs-ccts/downloads
 cd ..
 tar xzvf downloads/cgatools-
 # create module file
 emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-
 # edit, edit edit

download reference genomes from CG

download reference data

 cd /scratch/share/public_datasets/ngs/databases/completegenomics

validate downloaded .crr

 cd /scratch/share/ngs/databases/completegenomics
 module load ngs-ccts/completegenomics-cgatools-1.7.1
 # list contents
 cgatools listcrr --reference ReferenceFiles/build${BUILD}.crr > build${BUILD}.listcrr.out
 diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out
 # extract some sequence
 cgatools decodecrr --reference ReferenceFiles/build${BUILD}.crr --range chr16:10000000-10000050