NgsCctsBuildCompleteGenomics

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(1.7.1 (2013-08-29))
(download reference genomes from CG)
Line 16: Line 16:
 
== download reference genomes from CG ==
 
== download reference genomes from CG ==
  
{{{
+
download reference data
cd /scratch/share/ngs/databases/completegenomics
+
  cd /scratch/share/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
+
validate downloaded .crr
BUILD=36
+
  BUILD=36
cd /scratch/share/ngs/databases/completegenomics
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  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
+
  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
}}}
+

Revision as of 15:47, 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

download reference data

 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
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