recipe gimbleprep

Preprocess fasta, bam and vcf files ready to be used by gimble

Homepage:

https://github.com/LohseLab/gimbleprep

License:

GPL3 / GPL-3.0-or-later

Recipe:

/gimbleprep/meta.yaml

package gimbleprep

versions:

0.0.2-0,  0.0.2b6-0,  0.0.2b5-0,  0.0.2b4-0,  0.0.2b3-0

depends bcftools:

depends bedtools:

depends docopt:

depends mosdepth:

0.3.2

depends numpy:

depends pandas:

depends parallel:

depends pysam:

depends python:

>=3.8

depends samtools:

depends tqdm:

depends vcflib:

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 gimbleprep

and update with::

   mamba update gimbleprep

To create a new environment, run:

mamba create --name myenvname gimbleprep

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/gimbleprep:<tag>

(see `gimbleprep/tags`_ for valid values for ``<tag>``)

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