recipe cgat-apps

Computational Genomics Analysis Toolkit

Homepage:

https://cgat-apps.readthedocs.io/en/latest/

License:

MIT

Recipe:

/cgat-apps/meta.yaml

package cgat-apps

versions:

0.6.5-3,  0.6.5-2,  0.6.5-1,  0.6.5-0,  0.6.4-1,  0.6.4-0,  0.6.0-2,  0.6.0-1,  0.6.0-0, 

0.6.5-3,  0.6.5-2,  0.6.5-1,  0.6.5-0,  0.6.4-1,  0.6.4-0,  0.6.0-2,  0.6.0-1,  0.6.0-0,  0.5.6-0,  0.5.5-0,  0.5.4-0,  0.5.3-0

depends alignlib-lite:

depends bedtools:

depends biopython:

depends cgatcore:

>=0.6.5

depends coreutils:

depends future:

depends grep:

depends htslib:

>=1.16,<1.19.0a0

depends jinja2:

depends libcxx:

>=14.0.4

depends matplotlib-base:

depends numpy:

>=1.21.6,<2.0a0

depends pandas:

depends pybedtools:

depends pybigwig:

depends pysam:

>=0.17.0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends pyyaml:

depends quicksect:

depends scikit-learn:

depends scipy:

depends six:

depends sortedcontainers:

depends ucsc-bedgraphtobigwig:

depends ucsc-bedtobigbed:

depends ucsc-wigtobigwig:

depends zlib:

>=1.2.12,<1.3.0a0

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 cgat-apps

and update with::

   mamba update cgat-apps

To create a new environment, run:

mamba create --name myenvname cgat-apps

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/cgat-apps:<tag>

(see `cgat-apps/tags`_ for valid values for ``<tag>``)

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