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

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

Versions

2.20.6-0, 2.20.5-0, 2.20.4-1, 2.20.4-0, 2.20.3-0, 2.20.2-0, 2.20.1-0, 2.20.0-0, 2.19.2-0, 2.19.1-0, 2.19.0-0, 2.18.29-0, 2.18.27-0, 2.18.26-0, 2.18.25-0, 2.18.23-0, 2.18.22-0, 2.18.21-0, 2.18.20-0, 2.18.17-0, 2.18.16-0, 2.18.15-0, 2.18.14-0, 2.18.13-0, 2.18.12-0, 2.18.11-0, 2.18.10-0, 2.18.9-0, 2.18.7-2, 2.18.7-0, 2.18.6-0, 2.18.5-0, 2.18.4-0, 2.18.3-0, 2.18.2-0, 2.18.1-0, 2.18.0-0, 2.17.11-0, 2.17.10-0, 2.17.8-0, 2.17.6-0, 2.17.5-0, 2.17.4-0, 2.17.3-0, 2.17.2-0, 2.17.0-0, 2.16.0-0, 2.15.0-0, 2.14.1-0, 2.14-0, 2.13-1, 2.13-0, 2.11.0-0, 2.10.6-0, 2.9.2-2, 2.9.2-1, 2.9.2-0, 2.9.0-0, 2.7.1-2, 2.7.1-1, 2.7.1-0, 2.5.0-2, 2.5.0-1, 2.5.0-0, 2.3.0-0, 2.0.1-1, 2.0.1-0, 1.141-4, 1.141-3, 1.141-1, 1.141-0, 1.139-0, 1.126-5, 1.126-4, 1.126-3, 1.126-2, 1.97-0, 1.56-1, 1.56-0

Depends

• openjdk >=8

• r-base

Required By

• phyluce

• wgfast

• lohhla

• cap-mirseq

• uvp

• wg-blimp

• fusioncatcher

• shiver

• batvi

• secapr

• ctat-mutations

• hla-la

• mtbseq

• phenix

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install picard

and update with:

conda update picard

or use the docker container:

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

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

Link to this page

Render an 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/README.html)