Mercurial > repos > galaxyp > reactome_pathwaymatcher

view README.rst @ 1:5d0c44bc354d 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 7e04827e48352f6b28cf2e2c93a89a270e5bf026
author galaxyp
date Wed, 04 Jul 2018 04:28:07 -0400
parents f66af2b04a98
children 9a599f278852
line wrap: on
line source

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

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