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Software for Long-Read Sequencing Data from PacBio.



See which versions of pbsuite are available:

$ module avail pbsuite

Load one version of pbsuite into your environment:

$ module load pbsuite/15.8.24


Notes from the sysadmin during installation:

$ cd /tmp
$ wget '' -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/{,,}
$ 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 on the PBSuite discussion board.

pbsuite-software.txt · Last modified: 2017/09/30 06:35 by aorth