NgsCctsBuildCompleteGenomics

= Binary install of Complete Genomics Analysis Tools =

Source http://sourceforge.net/projects/cgatools/files/

1.7.1 (2013-08-29)
# binary download cd /share/apps/ngs-ccts/downloads wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz/download cd .. tar xzvf downloads/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz # create module file emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.7.1.5 # edit, edit edit

download reference genomes from CG
download reference data cd /scratch/share/public_datasets/ngs/databases/completegenomics qsub cg_download_36.sh qsub cg_download_37.sh

validate downloaded .crr BUILD=36 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

1.5.0 (2013-08-29)
Why? This is the last version to support map2sam!!

# binary download cd /share/apps/ngs-ccts/downloads wget http://sourceforge.net/projects/cgatools/files/1.5.0/cgatools-1.5.0.31-linux_binary-x86_64.tar.gz/download cd .. tar xzvf downloads/cgatools-1.5.0.31-linux_binary-x86_64.tar.gz # create module file cd /share/apps/ngs-ccts/modulefiles cp completegenomics-cgatools-1.7.1 completegenomics-cgatools-1.5.0 emacs -nw /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.5.0 # edit, edit edit