NgsCctsBuildCompleteGenomics: Difference between revisions
Jump to navigation
Jump to search
(Created page with "= Binary install of Complete Genomics Analysis Tools = Source http://sourceforge.net/projects/cgatools/files/ == 1.7.1 (2013-08-29) == {{{ cd /share/apps/ngs-ccts/download...") |
|||
| (5 intermediate revisions by the same user not shown) | |||
| Line 5: | Line 5: | ||
== 1.7.1 (2013-08-29) == | == 1.7.1 (2013-08-29) == | ||
# binary download | |||
cd /share/apps/ngs-ccts/downloads | 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 | wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz/download | ||
cd .. | cd .. | ||
tar xzvf downloads/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz | tar xzvf downloads/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz | ||
emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.7.1.5 | # create module file | ||
# edit, edit edit | emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.7.1.5 | ||
# edit, edit edit | |||
== download reference genomes from CG == | == download reference genomes from CG == | ||
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 | ||
validate downloaded .crr | |||
BUILD=36 | BUILD=36 | ||
cd /scratch/share/ngs/databases/completegenomics | cd /scratch/share/ngs/databases/completegenomics | ||
module load ngs-ccts/completegenomics-cgatools-1.7.1 | module load ngs-ccts/completegenomics-cgatools-1.7.1 | ||
cgatools listcrr --reference ReferenceFiles build${BUILD}.crr > build${BUILD}.listcrr.out | # list contents | ||
diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out | 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${BUILD}.crr --range chr16:10000000-10000050 | |||
== 1.5.0 (2013-08-29) == | |||
Why? This is the last version to support map2sam!! | |||
# binary download | |||
cd /share/apps/ngs-ccts/downloads | |||
wget http://sourceforge.net/projects/cgatools/files/1.5.0/cgatools-1.5.0.31-linux_binary-x86_64.tar.gz/download | |||
cd .. | |||
tar xzvf downloads/cgatools-1.5.0.31-linux_binary-x86_64.tar.gz | |||
# create module file | |||
cd /share/apps/ngs-ccts/modulefiles | |||
cp completegenomics-cgatools-1.7.1 completegenomics-cgatools-1.5.0 | |||
emacs -nw /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.5.0 | |||
# edit, edit edit | |||
Latest revision as of 03:53, 30 August 2013
Binary install of Complete Genomics Analysis Tools
Source http://sourceforge.net/projects/cgatools/files/
1.7.1 (2013-08-29)
# binary download cd /share/apps/ngs-ccts/downloads wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz/download cd .. tar xzvf downloads/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz # create module file emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.7.1.5 # edit, edit edit
download reference genomes from CG
download reference data
cd /scratch/share/public_datasets/ngs/databases/completegenomics qsub cg_download_36.sh qsub cg_download_37.sh
validate downloaded .crr
BUILD=36
cd /scratch/share/ngs/databases/completegenomics
module load ngs-ccts/completegenomics-cgatools-1.7.1
# list contents
cgatools listcrr --reference ReferenceFiles/build${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