NgsCctsBuildCompleteGenomics: Difference between revisions
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| Line 17: | Line 17: | ||
download reference data | download reference data | ||
cd /scratch/share/ngs/databases/completegenomics | cd /scratch/share/public_datasets/ngs/databases/completegenomics | ||
qsub cg_download_36.sh | qsub cg_download_36.sh | ||
qsub cg_download_37.sh | qsub cg_download_37.sh | ||
| Line 27: | Line 27: | ||
module load ngs-ccts/completegenomics-cgatools-1.7.1 | module load ngs-ccts/completegenomics-cgatools-1.7.1 | ||
# list contents | # list contents | ||
cgatools listcrr --reference ReferenceFiles build${BUILD}.crr > build${BUILD}.listcrr.out | cgatools listcrr --reference ReferenceFiles/build${BUILD}.crr > build${BUILD}.listcrr.out | ||
diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out | diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out | ||
# 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 | ||
Revision as of 03:47, 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