NgsCctsBuildCompleteGenomics

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(download reference genomes from CG)
(1.5.0 (2013-08-29))
 
(3 intermediate revisions by one user not shown)
Line 17: Line 17:
  
 
download reference data
 
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
Line 26: Line 26:
 
   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
 +
   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
 +
  # 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 21:53, 29 August 2013

Contents

[edit] Binary install of Complete Genomics Analysis Tools

Source http://sourceforge.net/projects/cgatools/files/

[edit] 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

[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

[edit] 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
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