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...")
 
(1.5.0 (2013-08-29))
 
(5 intermediate revisions by one user not shown)
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 ==
  
{{{
+
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
}}}
+
  
{{{
+
 
# validate downloaded .crr
+
validate downloaded .crr
BUILD=36
+
  BUILD=36
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
diff build${BUILD}.listcrr.ref build${BUILD}.listcrr.out
+
  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

Latest revision as of 22:53, 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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