recipe bioconductor-msbackendsql

SQL-based Mass Spectrometry Data Backend

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MsBackendSql.html

License:

Artistic-2.0

Recipe:

/bioconductor-msbackendsql/meta.yaml

SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.

package bioconductor-msbackendsql

versions:

1.2.0-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-mscoreutils:

>=1.14.0,<1.15.0

depends bioconductor-protgenerics:

>=1.34.0,<1.35.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-spectra:

>=1.12.0,<1.13.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dbi:

depends r-progress:

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 bioconductor-msbackendsql

and update with::

   mamba update bioconductor-msbackendsql

To create a new environment, run:

mamba create --name myenvname bioconductor-msbackendsql

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/bioconductor-msbackendsql:<tag>

(see `bioconductor-msbackendsql/tags`_ for valid values for ``<tag>``)

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Link to this page

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