pbsuite-software
Table of Contents
PBSuite
Software for Long-Read Sequencing Data from PacBio.
Information
- Version: 15.8.24
- Added: September, 2017
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 06:35 by aorth