recipe picard

Java tools for working with NGS data in the BAM format

Homepage:

http://broadinstitute.github.io/picard/

Developer docs:

https://github.com/broadinstitute/picard

License:

MIT / MIT

Recipe:

/picard/meta.yaml

Links:

usegalaxy-eu: picard_MarkDuplicates

Java tools for working with NGS data in the BAM format. This package depends on 'r-base' because Picard requires R to run some of its metrics commands. The 'picard-slim' package offers an installation of Picard without the 'r-base' dependency.

package picard

(downloads) docker_picard

versions:
3.1.1-03.1.0-03.0.0-13.0.0-02.27.5-02.27.4-02.27.3-02.27.2-02.27.1-0

3.1.1-03.1.0-03.0.0-13.0.0-02.27.5-02.27.4-02.27.3-02.27.2-02.27.1-02.27.0-02.26.11-02.26.10-02.26.9-02.26.8-02.26.7-02.26.6-02.26.5-02.26.4-02.26.3-02.26.2-02.26.1-02.26.0-02.25.7-02.25.6-02.25.5-02.25.4-02.25.3-02.25.2-02.25.1-12.25.1-02.25.0-12.25.0-02.24.2-02.24.1-02.24.0-02.23.9-02.23.8-02.23.7-02.23.6-02.23.5-02.23.4-02.23.3-02.23.2-02.23.1-02.23.0-02.22.9-02.22.8-02.22.7-02.22.6-02.22.5-02.22.4-02.22.3-02.22.2-02.22.1-02.22.0-02.21.9-02.21.8-02.21.7-02.21.6-02.21.5-02.21.4-02.21.3-02.21.2-12.21.2-02.21.1-02.20.8-02.20.7-02.20.6-02.20.5-02.20.4-12.20.4-02.20.3-02.20.2-02.20.1-02.20.0-02.19.2-02.19.1-02.19.0-02.18.29-02.18.27-02.18.26-02.18.25-02.18.23-02.18.22-02.18.21-02.18.20-02.18.17-02.18.16-02.18.15-02.18.14-02.18.13-02.18.12-02.18.11-02.18.10-02.18.9-02.18.7-22.18.7-02.18.6-02.18.5-02.18.4-02.18.3-02.18.2-02.18.1-02.18.0-02.17.11-02.17.10-02.17.8-02.17.6-02.17.5-02.17.4-02.17.3-02.17.2-02.17.0-02.16.0-02.15.0-02.14.1-02.14-02.13-12.13-02.11.0-02.10.6-02.9.2-22.9.2-12.9.2-02.9.0-02.7.1-22.7.1-12.7.1-02.5.0-22.5.0-12.5.0-02.3.0-02.0.1-12.0.1-01.141-61.141-51.141-41.141-31.141-11.141-01.139-01.126-51.126-41.126-31.126-21.97-01.56-11.56-0

depends openjdk:

>=17

depends r-base:

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 picard

and update with::

   mamba update picard

To create a new environment, run:

mamba create --name myenvname picard

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/picard:<tag>

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

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