recipe pathwaymatcher

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

Homepage:

https://github.com/PathwayAnalysisPlatform/PathwayMatcher

License:

Apache License, Version 2.0

Recipe:

/pathwaymatcher/meta.yaml

package pathwaymatcher

versions:

1.9.1-3,  1.9.1-2,  1.9.1-1,  1.8.1-2,  1.8.1-1,  1.8-1,  1.7-0

depends openjdk:

>=8

depends python:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pathwaymatcher

and update with::

   mamba update pathwaymatcher

To create a new environment, run:

mamba create --name myenvname pathwaymatcher

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pathwaymatcher:<tag>

(see `pathwaymatcher/tags`_ for valid values for ``<tag>``)

Notes

PathwayMatcher is Java program that comes with a custom wrapper shell script. By default "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "java -Xms512m -Xmx1g -jar PathwayMatcher.jar"

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