Mercurial > repos > galaxyp > reactome_pathwaymatcher

view README.rst @ 0:f66af2b04a98 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 c12a99d3da62c83b779175b3c9022e7d5622053a
author galaxyp
date Wed, 20 Jun 2018 14:21:10 -0400
parents
children 5d0c44bc354d
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 1.6 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'

On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example:

	export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M'

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>