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:

2.13.2-3,  2.13.2-2,  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, 

2.13.2-3,  2.13.2-2,  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:

depends bcftools:

depends bioconductor-structuralvariantannotation:

>=1.6

depends bwa:

>=0.7

depends entrez-direct:

depends htslib:

>=1.19.1,<1.21.0a0

depends kraken2:

>=2.1

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends ncurses:

>=6.4,<7.0a0

depends openjdk:

>=8

depends r-argparser:

depends r-base:

>=4.0

depends r-stringdist:

depends r-testthat:

depends r-tidyverse:

depends repeatmasker:

>=4.1.1

depends samtools:

>=1.14

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 gridss

and update with::

   mamba update gridss

To create a new environment, run:

mamba create --name myenvname gridss

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/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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