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pbsuite-software [2017/09/30 06:30]
aorth [Usage]
pbsuite-software [2017/09/30 06:35]
aorth
Line 31: Line 31:
 $ pip install networkx==1.7 numpy pyparsing $ pip install networkx==1.7 numpy pyparsing
 $ chmod +x bin/sawriter $ chmod +x bin/sawriter
 +# manually edit all short style blasr parameters in pbsuite/jelly/{Assembly.py,m4pie.py,Stages.py}
 $ cp -r * /export/apps/pbsuite/15.8.24 $ cp -r * /export/apps/pbsuite/15.8.24
 $ sudo chown -R root:root /export/apps/pbsuite/15.8.24</code> $ sudo chown -R root:root /export/apps/pbsuite/15.8.24</code>
  
 Note: the [[https://sourceforge.net/p/pb-jelly/wiki/Home/|PBJelly wiki readme]] says to install networkx 1.1, but then the included readme says to use 1.7. Note: the [[https://sourceforge.net/p/pb-jelly/wiki/Home/|PBJelly wiki readme]] says to install networkx 1.1, but then the included readme says to use 1.7.
 +
 +Also note: PBSuite is very old and uses incompatible command-line options for modern versions of blasr. You need to make sure you're using long-form options like ''--sa'' and ''--out'' instead of ''-sa'' and ''-out''. See [[this thread|https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/7657e087/]] on the PBSuite discussion board.
pbsuite-software.txt · Last modified: 2017/09/30 06:35 by aorth