Mercurial > repos > galaxyp > reactome_pathwaymatcher

view README.rst @ 2:03487adf8fc2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
author galaxyp
date Thu, 26 Jul 2018 17:00:22 -0400
parents ee1dfac35bb3
children
line wrap: on
line source

PathwayMatcher
=======================

- Home: <https://github.com/PathwayAnalysisPlatform/PathwayMatcher>
- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/reactome_pathwaymatcher>
- Tools ID: `reactome_pathwaymatcher`


Description
-----------

PathwayMatcher is a software tool written in Java to search for pathways related to a list of proteins in Reactome.


General Requirements
--------------------

This tool requires a Java runtime 1.8 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:

    export _JAVA_OPTIONS='-Xmx1500M'

It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.


License
-------

PathwayMatcher is a free open-source project, following an Apache License 2.0.


Authors
-------

Authors and contributors:

* Luis Francisco Hernández Sánchez <luis.sanchez@uib.no>
* Carlos Horro Marcos <carlos.horro@uib.no>