User Tools

Site Tools


pbsuite-software

PBSuite

Software for Long-Read Sequencing Data from PacBio.

Information

Usage

See which versions of pbsuite are available:

$ module avail pbsuite

Load one version of pbsuite into your environment:

$ module load pbsuite/15.8.24

Installation

Notes from the sysadmin during installation:

$ 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

Note: the 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/ on the PBSuite discussion board.

pbsuite-software.txt · Last modified: 2017/09/30 09:35 by aorth