Bioinformatics for Cancer Genomics Somatic Mutations Lab 2015

Workshop pages for students

Lab Module 6 - Software Installation Instructions

This page describes where to get and how to install the software used for this lab module.

Installing Strelka

We can retrieve Strelka from its website.

tar -xzvf strelka_workflow-1.0.14.tar.gz

Now we run configure and make on it:

cd strelka_workflow-1.0.14
./configure --prefix=/path/to/strelka

Installing MutationSeq

We can retrieve MutationSeq from its website.

wget ftp://ftp.bcgsc.ca/public/shahlab/MutationSeq/museq.zip
unzip museq.zip

We will need a working installation of python that has the appropriate analytical packages. The easiest way to get this is to install Anaconda. This distribution of Python contains all the analytical packages needed by MutationSeq.

Once you have this installed, you’ll need to edit the makefile in the museq folder, the line you need to change is:

/share/lustre/jtaghiyar/Apps/python/bin/python2.7 setup.py --boost_source=$(BOOSTPATH) install --prefix=./ --install-platlib=./

You’ll need to replace /share/lustre/jtaghiyar/Apps/python/bin/python2.7 with the python you want to use. The $(BOOSTPATH) needs to point to the path where you installed Boost.

Once you’ve edited this line, you can enter make in the museq folder and it should be the pybam.so which is what you need for MutationSeq to work.

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