NgsCctsBuildCompleteGenomics: Difference between revisions
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# extract some sequence | # extract some sequence | ||
cgatools decodecrr --reference ReferenceFiles/build${BUILD}.crr --range chr16:10000000-10000050 | cgatools decodecrr --reference ReferenceFiles/build${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 |
Revision as of 03:53, 30 August 2013
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