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:
4.6.2.0-1,  4.6.2.0-0,  4.6.1.0-0,  4.5.0.0-0,  4.4.0.0-0,  4.3.0.0-0,  4.2.6.1-1,  4.2.6.1-0,  4.2.6.0-0, 

4.6.2.0-1,  4.6.2.0-0,  4.6.1.0-0,  4.5.0.0-0,  4.4.0.0-0,  4.3.0.0-0,  4.2.6.1-1,  4.2.6.1-0,  4.2.6.0-0,  4.2.5.0-0,  4.2.4.1-0,  4.2.4.0-0,  4.2.3.0-1,  4.2.3.0-0,  4.2.2.0-1,  4.2.2.0-0,  4.2.1.0-0,  4.2.0.0-1,  4.2.0.0-0,  4.1.9.0-0,  4.1.8.1-0,  4.1.8.0-0,  4.1.7.0-0,  4.1.6.0-0,  4.1.5.0-1,  4.1.5.0-0,  4.1.4.1-1,  4.1.4.1-0,  4.1.4.0-1,  4.1.4.0-0,  4.1.3.0-0,  4.1.2.0-1,  4.1.2.0-0,  4.1.1.0-0,  4.1.0.0-0,  4.0.12.0-0,  4.0.11.0-0,  4.0.10.0-0,  4.0.9.0-0,  4.0.8.1-0,  4.0.7.0-0,  4.0.6.0-0,  4.0.5.2-0,  4.0.5.1-0,  4.0.4.0-0,  4.0.3.0-1,  4.0.3.0-0,  4.0.2.1-0,  4.0.2.0-0,  4.0.1.2-0,  4.0.1.1-0,  4.0.1.0-0,  4.0.0.0-0,  4.0b6-0,  4.0b5-0,  4.0b4-0,  4.0b3-0,  4.0b2-0,  4.0b1-0,  4.0a1.2.7.2-2

Depends:

  • on openjdk >=17

  • on python >=3.10,<3.11.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install gatk4

to add into an existing workspace instead, run:

pixi add gatk4

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install gatk4

Alternatively, to install into a new environment, run:

conda create -n envname gatk4

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/gatk4:<tag>

(see gatk4/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

package gatk4-spark

(downloads) docker_gatk4-spark

Versions:
4.6.2.0-1,  4.6.2.0-0,  4.6.1.0-0,  4.5.0.0-0,  4.4.0.0-0,  4.3.0.0-0,  4.2.6.1-1,  4.2.6.1-0,  4.2.6.0-0, 

4.6.2.0-1,  4.6.2.0-0,  4.6.1.0-0,  4.5.0.0-0,  4.4.0.0-0,  4.3.0.0-0,  4.2.6.1-1,  4.2.6.1-0,  4.2.6.0-0,  4.2.5.0-0,  4.2.4.1-0,  4.2.4.0-0,  4.2.3.0-1,  4.2.3.0-0,  4.2.2.0-1,  4.2.2.0-0,  4.2.1.0-0,  4.2.0.0-1,  4.2.0.0-0,  4.1.9.0-0,  4.1.8.1-0,  4.1.8.0-0,  4.1.7.0-0,  4.1.6.0-0,  4.1.5.0-1,  4.1.5.0-0,  4.1.4.1-1,  4.1.4.1-0,  4.1.4.0-1,  4.1.4.0-0,  4.1.3.0-0,  4.1.2.0-1

Depends:

  • on gatk4 4.6.2.0 py310hdfd78af_1

  • on openjdk >=17

  • on python

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install gatk4-spark

to add into an existing workspace instead, run:

pixi add gatk4-spark

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install gatk4-spark

Alternatively, to install into a new environment, run:

conda create -n envname gatk4-spark

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/gatk4-spark:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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