NgsCctsBuildCompleteGenomics

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(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...")
 
(1.7.1 (2013-08-29))
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 15:46, 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 }}}

{{{

  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 }}}

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