NgsCctsBuildCompleteGenomics: Difference between revisions

From Cheaha
Jump to navigation Jump to search
 
(2 intermediate revisions by the same 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 27: Line 27:
   module load ngs-ccts/completegenomics-cgatools-1.7.1
   module load ngs-ccts/completegenomics-cgatools-1.7.1
   # list contents
   # list contents
   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
   # extract some sequence
   # extract some sequence
   cgatools decodecrr --reference ReferenceFiles/build${BUILD}.crr --range chr16:10000000-10000050
   cgatools decodecrr --reference ReferenceFiles/build${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 03:53, 30 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/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

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