recipe cgat-scripts

Computational Genomics Analysis Toolkit

Homepage:

https://www.cgat.org/downloads/public/cgat/documentation

License:

BSD

Recipe:

/cgat-scripts/meta.yaml

package cgat-scripts

versions:

0.3.2-2,  0.3.2-0,  0.3.1-1,  0.3.1-0,  0.3.0-0,  0.2.7-0,  0.2.6-0

depends alignlib-lite:

0.3.*

depends bedtools:

2.26.*

depends biopython:

1.70.*

depends coreutils:

8.25.*

depends cython:

0.27.*

depends future:

0.16.*

depends grep:

2.14.*

depends libgcc-ng:

>=4.9

depends libpng:

>=1.6.34,<1.7.0a0

depends matplotlib:

2.1.*

depends numpy:

1.12.*

depends pandas:

0.21.*

depends pybedtools:

0.7.*

depends pybigwig:

0.3.*

depends pysam:

0.13.*

depends python:

>=3.5,<3.6.0a0

depends python-lzo:

1.11.*

depends pyyaml:

3.12.*

depends rpy2:

2.8.*

depends scipy:

0.19.*

depends six:

1.11.*

depends ucsc-bedgraphtobigwig:

357.*

depends ucsc-bedtobigbed:

357.*

depends ucsc-wigtobigwig:

357.*

depends zlib:

>=1.2.11,<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-scripts

and update with::

   mamba update cgat-scripts

To create a new environment, run:

mamba create --name myenvname cgat-scripts

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-scripts:<tag>

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

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