recipe gatk4

Genome Analysis Toolkit (GATK4)

Homepage:

https://www.broadinstitute.org/gatk/

Developer docs:

https://github.com/broadinstitute/gatk

License:

BSD / BSD-3-Clause

Recipe:

/gatk4/meta.yaml

package gatk4

(downloads) docker_gatk4

versions:
4.4.0.0-04.3.0.0-04.2.6.1-14.2.6.1-04.2.6.0-04.2.5.0-04.2.4.1-04.2.4.0-04.2.3.0-1

4.4.0.0-04.3.0.0-04.2.6.1-14.2.6.1-04.2.6.0-04.2.5.0-04.2.4.1-04.2.4.0-04.2.3.0-14.2.3.0-04.2.2.0-14.2.2.0-04.2.1.0-04.2.0.0-14.2.0.0-04.1.9.0-04.1.8.1-04.1.8.0-04.1.7.0-04.1.6.0-04.1.5.0-14.1.5.0-04.1.4.1-14.1.4.1-04.1.4.0-14.1.4.0-04.1.3.0-04.1.2.0-14.1.2.0-04.1.1.0-04.1.0.0-04.0.12.0-04.0.11.0-04.0.10.0-04.0.9.0-04.0.8.1-04.0.7.0-04.0.6.0-04.0.5.2-04.0.5.1-04.0.4.0-04.0.3.0-14.0.3.0-04.0.2.1-04.0.2.0-04.0.1.2-04.0.1.1-04.0.1.0-04.0.0.0-04.0b6-04.0b5-04.0b4-04.0b3-04.0b2-04.0b1-04.0a1.2.7.2-2

depends openjdk:

>=17,<18

depends python:

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 gatk4

and update with::

   mamba update gatk4

To create a new environment, run:

mamba create --name myenvname gatk4

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/gatk4:<tag>

(see `gatk4/tags`_ for valid values for ``<tag>``)
package gatk4-spark

(downloads) docker_gatk4-spark

versions:
4.4.0.0-04.3.0.0-04.2.6.1-14.2.6.1-04.2.6.0-04.2.5.0-04.2.4.1-04.2.4.0-04.2.3.0-1

4.4.0.0-04.3.0.0-04.2.6.1-14.2.6.1-04.2.6.0-04.2.5.0-04.2.4.1-04.2.4.0-04.2.3.0-14.2.3.0-04.2.2.0-14.2.2.0-04.2.1.0-04.2.0.0-14.2.0.0-04.1.9.0-04.1.8.1-04.1.8.0-04.1.7.0-04.1.6.0-04.1.5.0-14.1.5.0-04.1.4.1-14.1.4.1-04.1.4.0-14.1.4.0-04.1.3.0-04.1.2.0-1

depends gatk4:

4.4.0.0 py36hdfd78af_0

depends openjdk:

>=17,<18

depends python:

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 gatk4-spark

and update with::

   mamba update gatk4-spark

To create a new environment, run:

mamba create --name myenvname gatk4-spark

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/gatk4-spark:<tag>

(see `gatk4-spark/tags`_ for valid values for ``<tag>``)

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