recipe fragpipe

Pipeline for comprehensive analysis of shotgun proteomics data

Homepage:

https://github.com/Nesvilab/FragPipe

License:

GPL-3.0 + LICENSE files

Recipe:

/fragpipe/meta.yaml

Links:

biotools: fragpipe, doi: 10.1074/mcp.TIR120.002048

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger - an ultrafast proteomic search engine suitable for both conventional and "open" (wide precursor mass tolerance) peptide identification. FragPipe includes the Philosopher toolkit for downstream post-processing of MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, label-based quantification, and multi-experiment summary report generation. Crystal-C and PTM-Shepherd are included to aid interpretation of open search results. Also included in FragPipe binary are TMT-Integrator for TMT/iTRAQ isobaric labeling-based quantification, IonQuant for label-free quantification with match-between-run (MBR) functionality, spectral library building with EasyPQP, and MSFragger-DIA and DIA-Umpire SE modules for direct analysis of data independent acquisition (DIA) data.

package fragpipe

(downloads) docker_fragpipe

versions:

20.0-4,  20.0-3,  20.0-2,  20.0-1,  20.0-0

depends easypqp:

>=0.1.34

depends ionquant:

>=1.10.12

depends lxml:

depends msfragger:

>=4.0

depends openjdk:

>=9

depends python:

3.9.*

depends zlib:

>=1.2.13

requirements:

additional platforms:

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 fragpipe

and update with::

   mamba update fragpipe

To create a new environment, run:

mamba create --name myenvname fragpipe

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/fragpipe:<tag>

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

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