Mercurial > repos > galaxyp > reactome_pathwaymatcher

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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
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1 PathwayMatcher
2 =======================
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4 - Home: <https://github.com/LuisFranciscoHS/PathwayMatcher/>
5 - Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/pathwaymatcher>
6 - Tools ID: `pathwaymatcher`
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9 Description
10 -----------
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12 PathwayMatcher is a software tool written in Java to search for pathways related to a list of proteins in Reactome.
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15 General Requirements
16 --------------------
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18 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:
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20 export _JAVA_OPTIONS='-Xmx1500M'
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22 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:
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24 export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M'
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26 It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.
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29 License
30 -------
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32 PathwayMatcher is a free open-source project, following an Apache License 2.0.
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35 Authors
36 -------
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38 Authors and contributors:
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40 * Luis Francisco Hernández Sánchez <luis.sanchez@uib.no>
41 * Carlos Horro Marcos <carlos.horro@uib.no>