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pbsuite-software [2017/09/30 06:25]
aorth created
pbsuite-software [2017/09/30 06:35]
aorth [Installation]
Line 13: Line 13:
 <code>$ module avail pbsuite</code> <code>$ module avail pbsuite</code>
  
-Load pbsuite into your environment: +Load one version of pbsuite into your environment: 
-<code>$ module load pbsuite</code>+<code>$ module load pbsuite/15.8.24</code>
  
 ===== Installation ====== ===== Installation ======
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 $ 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 [[https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/7657e087/|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