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# OpenMS

This repository is in an early alpha state and many OpenMS tools are
not yet available or are largely untested. If there is a tool that is
part of OpenMS but not available here, let John Chilton
([e-mail]) and he will try to add it.

These tools require Galaxy to be equipped with common proteomic
datatypes. These can be obtained by installing Ira Cooke's ProtK via
the tool shed or merging the changesets from the following repository
into your Galaxy instance:

     https://bitbucket.org/galaxyp/galaxy-dist-proteomics

# Installing

These tools all require OpenMS and may require other dependencies
(such as PepNovo for instance).

For Galaxy-P we are installing this tool via CloudBioLinux
(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio\
_proteomics.py). While
this fabric script may not be exactly appropriate for your environment
it may serve as a template for how to install this software.