NgsCctsBuildCompleteGenomics

From Cheaha
Revision as of 20:45, 29 August 2013 by Curtish@uab.edu (talk | contribs) (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...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.


Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/


Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

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/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 emacs /share/apps/ngs-ccts/modulefiles/completegenomics-cgatools-1.7.1.5

  1. edit, edit edit

}}}

download reference genomes from CG

{{{ cd /scratch/share/ngs/databases/completegenomics qsub cg_download_36.sh qsub cg_download_37.sh }}}

{{{

  1. 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 }}}