recipe proteomiqon-peptidedb

The tool ProteomIQon.PeptideDB creates a peptide database in the SQLite format.

Homepage:

https://csbiology.github.io/ProteomIQon/

Documentation:

https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html

Developer docs:

https://github.com/CSBiology/ProteomIQon

License:

MIT

Recipe:

/proteomiqon-peptidedb/meta.yaml

MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. An established method to identify acquired MS/MS spectra is the comparison of each spectrum with peptides in a reference database. The PeptideDB tool helps to create peptide databases by in silico digestion given proteome information in the FASTA format and a set of parameters that allow the user to mimic conditions of their specific experiment. The created database stores peptide protein relationships in a SQLite database which can then be supplied to other ProteomIQon tools.

package proteomiqon-peptidedb

(downloads) docker_proteomiqon-peptidedb

versions:

0.0.7-1,  0.0.7-0,  0.0.6-0,  0.0.4-0,  0.0.1-0

depends dotnet-runtime:

5.0.*

depends openssl:

1.1.*

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 proteomiqon-peptidedb

and update with::

   mamba update proteomiqon-peptidedb

To create a new environment, run:

mamba create --name myenvname proteomiqon-peptidedb

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/proteomiqon-peptidedb:<tag>

(see `proteomiqon-peptidedb/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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