recipe gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Homepage

https://github.com/PapenfussLab/gridss

License

GPL / GPL-3.0-only

Recipe

/gridss/meta.yaml

Links

biotools: gridss, doi: 10.1101/gr.222109.117, doi: 10.1186/s13059-021-02423-x

package gridss

Versions

2.13.2-1,  2.13.2-0,  2.13.1-0,  2.13.0-0,  2.12.2-0,  2.12.0-1,  2.12.0-0,  2.11.1-1,  2.11.1-0, 

2.13.2-1,  2.13.2-0,  2.13.1-0,  2.13.0-0,  2.12.2-0,  2.12.0-1,  2.12.0-0,  2.11.1-1,  2.11.1-0,  2.11.0-1,  2.11.0-0,  2.10.2-0,  2.10.1-0,  2.10.0-0,  2.9.4-0,  2.9.3-0,  2.9.2-0,  2.9.1-0,  2.8.3-0,  2.8.2-0,  2.8.1-0,  2.8.0-1,  2.8.0-0,  2.7.3-0,  2.7.2-0,  2.7.1-0,  2.7.0-0,  2.6.3-0,  2.6.2-0,  2.6.1-0,  2.6.0-0,  2.5.2-0,  2.5.1-0,  2.1.0-0,  2.0.1-0,  1.9.0-0,  1.8.1-0,  1.8.0-0,  1.7.2-2,  1.7.2-0,  1.3.4-0,  1.3.2-0,  1.3.0-0,  1.2.4-0

Depends

• bc

• bcftools

• bioconductor-structuralvariantannotation >=1.6

• bwa >=0.7

• entrez-direct

• htslib >=1.15,<1.16.0a0

• kraken2 >=2.1

• libgcc-ng >=10.3.0

• libzlib >=1.2.11,<1.3.0a0

• ncurses >=6.3,<7.0a0

• openjdk >=8

• r-argparser

• r-base >=4.0

• r-stringdist

• r-testthat

• r-tidyverse

• repeatmasker >=4.1.1

• samtools >=1.14

• zlib >=1.2.11,<1.3.0a0

Required By

Installation

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

conda install gridss

and update with:

conda update gridss

or use the docker container:

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

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

Notes

The package contains additional command line wrappers for the GRIDSS java-based utilities.

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