recipe hmftools-sage

SAGE is a somatic SNV, MNV and small INDEL caller optimised 100x tumor / 40x normal coverage, but has a flexible set of filters that can be adapted to lower or higher depth coverage.

Homepage:

https://github.com/hartwigmedical/hmftools/tree/master/sage

License:

GPL / GPL-3.0-only

Recipe:

/hmftools-sage/meta.yaml

package hmftools-sage

(downloads) docker_hmftools-sage

versions:
4.0_beta-3,  4.0_beta-2,  4.0_beta-1,  4.0_beta-0,  3.4.4-0,  3.4.3-0,  3.4.2-0,  3.4.1-0,  3.4-1, 

4.0_beta-3,  4.0_beta-2,  4.0_beta-1,  4.0_beta-0,  3.4.4-0,  3.4.3-0,  3.4.2-0,  3.4.1-0,  3.4-1,  3.4-0,  3.2.3-0,  3.1-0,  3.0.3-0,  3.0.2-0,  3.0.1-0,  2.8-1,  2.8-0,  2.7-1,  2.7-0,  2.6-0,  2.5-0,  2.4-0,  2.3-0,  2.2-2,  2.2-1,  2.2-0,  1.0-0

depends bioconductor-genomicranges:

depends bioconductor-variantannotation:

depends font-ttf-dejavu:

depends openjdk:

>=9

depends r-dplyr:

depends r-ggplot2:

depends r-patchwork:

depends r-tidyr:

depends xorg-libxt:

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 hmftools-sage

and update with::

   mamba update hmftools-sage

To create a new environment, run:

mamba create --name myenvname hmftools-sage

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/hmftools-sage:<tag>

(see `hmftools-sage/tags`_ for valid values for ``<tag>``)

Download stats

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/hmftools-sage/README.html)