recipe psm-utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results.

Homepage:

https://github.com/compomics/psm_utils

Documentation:

https://psm_utils.readthedocs.io

License:

APACHE / Apache-2.0

Recipe:

/psm-utils/meta.yaml

Links:

doi: 10.1021/acs.jproteome.2c00609, biotools: psm_utils

package psm-utils

versions:

1.2.0-1,  1.2.0-0,  1.1.1-0,  1.1.0-0,  1.0.1-0,  1.0.0-0,  0.9.0-0,  0.8.3-0,  0.8.2-0, 

1.2.0-1,  1.2.0-0,  1.1.1-0,  1.1.0-0,  1.0.1-0,  1.0.0-0,  0.9.0-0,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.8.0-0,  0.7.4-0,  0.7.3-1,  0.7.3-0,  0.7.2-0,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.0-0,  0.5.0-0,  0.4.1-0,  0.2.3-0,  0.2.1-0,  0.2.0-0,  0.1.0-0

depends click:

depends lxml:

depends numpy:

depends pandas:

depends psims:

depends pyarrow:

depends pydantic:

depends pyopenms:

depends pyteomics:

>=4

depends python:

>=3.7

depends rich:

depends sqlalchemy:

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 psm-utils

and update with::

   mamba update psm-utils

To create a new environment, run:

mamba create --name myenvname psm-utils

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/psm-utils:<tag>

(see `psm-utils/tags`_ for valid values for ``<tag>``)

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