http://genomics.princeton.edu/AndolfattoLab/MSG.html https://github.com/JaneliaSciComp/msg http://www.ncbi.nlm.nih.gov/pubmed/21233398

This version is outdated

See dev branch for the latest version. It has had improvements merged from the fork at https://github.com/YourePrettyGood/msg, on their dev branch. In addition, it has been containerized. See the README on dev branch for details.

Run test_dependencies.sh to check for the existence of dependencies

NOTE: Most of these packages can be found in the dependencies directory for you to extract and install as needed on your system.

Python (2.6.4) numpy (recent versions should be fine) bwa (0.5.7) samtools (0.1.9-3) ! Newer versions of Samtools will not work ! biopython-1.53 Pyrex-0.9.9 pysam-0.1.2 (apply fix as described here: http://code.google.com/p/pysam/issues/detail?id=22&can=1&q=dandavison0) R-3.3.1 R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 3_1.7.1 and R.oo 1.20.0) Perl Modules (IO::Uncompress::Gunzip) -- A command like this should work on Unix Desktop Systems: -- perl -MCPAN -e 'install IO::Uncompress::Gunzip' mailer (Python package: http://pypi.python.org/pypi/mailer) - optional; for sending email alert when run completes

git clone git://github.com/JaneliaSciComp/msg.git cd msg make

The toy example is useful to check that MSG and dependencies are installed and functioning correctly. TODO

Download the data from NCBI's Sequence Read Archive and MSG config and barcodes file

• example/get_sample_data.sh (requires wget)