recipe pia

PIA is a toolbox for MS based protein inference and identification analysis.

Homepage:

https://github.com/medbioinf/pia

License:

BSD-3-Clause

Recipe:

/pia/meta.yaml

Links:

biotools: pia, doi: 10.1021/acs.jproteome.5b00121

PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins.

package pia

(downloads) docker_pia

versions:

1.5.0-0,  1.4.10-1,  1.4.10-0,  1.4.9-0,  1.4.8-0

depends openjdk:

>=21

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 pia

and update with::

   mamba update pia

To create a new environment, run:

mamba create --name myenvname pia

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/pia:<tag>

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

Notes

PIA is Java program that comes with a custom wrapper shell script. This shell wrapper is called "pia" and is on $PATH by default. By default "-Xms2g -Xmx4g" 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 "pia -Xms512m -Xmx2g" for a lower memory footprint.

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