recipe ggd

GoGetData (GGD) is a genomic data managment system. It provide simple and reproducible access to a repository of genomic data. Simply put, it is 'Conda' for genomic data

Homepage:

https://github.com/gogetdata/ggd-cli

License:

MIT

Recipe:

/ggd/meta.yaml

package ggd

versions:

1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.1.3-0,  0.1.2-1, 

1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.1.3-0,  0.1.2-1,  0.1.2-0,  0.1.1-1,  0.1.1-0,  0.1.0-1,  0.1.0-0

depends check-sort-order:

>=0.0.7

depends conda:

>=4.8.2,<=4.9.0

depends conda-build:

>=3.18.12,<=3.19.3

depends cyvcf2:

depends future:

depends fuzzywuzzy:

depends git:

depends gitpython:

depends gsort:

>=0.1.4

depends htslib:

depends krb5:

depends oyaml:

depends pysam:

depends pytest:

depends pytest-socket:

depends python:

depends python-levenshtein:

depends pyyaml:

depends requests:

>=2.22.*

depends ripgrep:

depends samtools:

>=1.10

depends wget:

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 ggd

and update with::

   mamba update ggd

To create a new environment, run:

mamba create --name myenvname ggd

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/ggd:<tag>

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

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