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...") |
|||
| 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 == | ||
Revision as of 20:46, 29 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
{{{ cd /scratch/share/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 cgatools listcrr --reference ReferenceFiles build${BUILD}.crr > build${BUILD}.listcrr.out diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out }}}