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--- pbsuite-software [2017/09/30 06:25]
aorth created
+++ pbsuite-software [2017/09/30 06:35] (current)
aorth [Installation]
@@ Line 13: / Line 13: @@
 <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 ======
@@ Line 31: / Line 31: @@
 $ pip install networkx==1.7 numpy pyparsing
 $ 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
 $ 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.
+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.

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