GotCloud: Alignment Pipeline: Difference between revisions

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Created page with 'Login as a normal user (not as root) and do: # Test the aligner (fast, about 3 minutes) /usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign rm -rf ~/testalign …'
 
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Login as a normal user (not as root) and do:
Back to the beginning [http://genome.sph.umich.edu/wiki/Pipelines]


#  Test the aligner (fast, about 3 minutes)
Running the aligner is straightforward:
/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
 
  rm -rf ~/testalign              # If no error
<code>
  '''cd ~/myseq'''
#  Test umake  (longer, about 15 minutes)
  ''' /usr/local/biopipe/bin/gen_biopipeline.pl -out aligner -index ???
  /usr/local/biopipe/bin/umake.pl --test ~/testumake
</code>
rm -rf ~/testumake              # If no error

Revision as of 10:13, 29 October 2012

Back to the beginning [1]

Running the aligner is straightforward: 

cd ~/myseq
 /usr/local/biopipe/bin/gen_biopipeline.pl -out aligner -index ???

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=GotCloud:_Alignment_Pipeline&oldid=5668"