ILRI Research Computing

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== PBSuite ======
Software for Long-Read Sequencing Data from PacBio.

===== Information =====

  * Version: 15.8.24
  * Added: September, 2017
  * Link: https://sourceforge.net/projects/pb-jelly/

===== Usage =====

See which versions of pbsuite are available:
<code>$ module avail pbsuite</code>

Load one version of pbsuite into your environment:
<code>$ module load pbsuite/15.8.24</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget 'https://downloads.sourceforge.net/project/pb-jelly/PBSuite_15.8.24.tgz?r=https%3A%2F%2Fsourceforge.net%2Fp%2Fpb-jelly%2Fwiki%2FHome%2F&ts=1506513538&use_mirror=netix' -O PBSuite_15.8.24.tgz
$ tar xf PBSuite_15.8.24.tgz
$ cd PBSuite_15.8.24
$ sudo mkdir -p /export/apps/pbsuite/15.8.24
$ sudo chown aorth /export/apps/pbsuite/15.8.24
$ module load python/2.7.13
$ python -m virtualenv /export/apps/pbsuite/15.8.24
$ . /export/apps/pbsuite/15.8.24/bin/activate
$ pip install -U pip setuptools
$ 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.