- recipe pia
PIA is a toolbox for MS based protein inference and identification analysis.
- Homepage:
- License:
BSD-3-Clause
- Recipe:
- 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¶
- Versions:
1.5.8-0,1.5.7-0,1.5.6-0,1.5.5-2,1.5.5-0,1.5.4-0,1.5.3-0,1.5.2-0,1.5.1-0,1.5.8-0,1.5.7-0,1.5.6-0,1.5.5-2,1.5.5-0,1.5.4-0,1.5.3-0,1.5.2-0,1.5.1-0,1.5.0-0,1.4.10-1,1.4.10-0,1.4.9-0,1.4.8-0- Depends:
on openjdk
21.*
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install pia
to add into an existing workspace instead, run:
pixi add pia
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install pia
Alternatively, to install into a new environment, run:
conda create -n envname pia
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/pia:<tag>
(see pia/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pia/README.html)
