recipe picard-slim

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-slim/meta.yaml

Links:

usegalaxy-eu: picard_MarkDuplicates

Java tools for working with NGS data in the BAM format. This package lacks the R dependency that is only required for some metrics tasks. This keeps the size of the package smaller, at the cost of breaking some of Picards's commands. The 'picard' package contains all the necessary dependencies.

package picard-slim

(downloads) docker_picard-slim

versions:
3.3.0-0,  3.2.0-0,  3.1.1-0,  3.1.0-0,  3.0.0-0,  2.27.4-0,  2.27.3-0,  2.27.2-0,  2.27.1-0, 

3.3.0-0,  3.2.0-0,  3.1.1-0,  3.1.0-0,  3.0.0-0,  2.27.4-0,  2.27.3-0,  2.27.2-0,  2.27.1-0,  2.27.0-0,  2.26.11-0,  2.26.10-0,  2.26.9-0,  2.26.8-0,  2.26.7-0,  2.26.6-0,  2.26.5-0,  2.26.4-0,  2.26.3-0,  2.26.2-0,  2.26.1-0,  2.26.0-0,  2.25.7-0,  2.25.6-0,  2.25.5-0,  2.25.4-0,  2.25.3-0,  2.25.2-0,  2.25.1-1,  2.25.1-0,  2.25.0-1,  2.25.0-0,  2.24.2-0,  2.24.1-0,  2.24.0-0,  2.23.9-0,  2.23.8-0,  2.23.7-0,  2.23.6-0,  2.23.5-0,  2.23.4-0,  2.23.3-0,  2.23.2-0,  2.23.1-0,  2.23.0-0,  2.22.9-0,  2.22.8-0,  2.22.7-0,  2.22.6-0,  2.22.5-0,  2.22.4-0,  2.22.3-0,  2.22.2-0,  2.22.1-0,  2.22.0-0,  2.21.9-0,  2.21.8-0,  2.21.7-0,  2.21.6-0,  2.21.5-0,  2.21.4-0,  2.21.3-0,  2.21.2-0,  2.21.1-0,  2.20.8-0,  2.20.7-0,  2.20.6-0,  2.20.5-0,  2.20.4-0

depends openjdk:

>=17

depends zlib:

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-slim

and update with::

   mamba update picard-slim

To create a new environment, run:

mamba create --name myenvname picard-slim

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-slim:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/picard-slim/README.html)