recipe hmftools-sv-prep

SV Prep generates a maximally filtered SV BAM file by identifying candidate SV junctions and extracting all reads that may provide support to that junction.

Homepage:

https://github.com/hartwigmedical/hmftools/tree/master/sv-prep

License:

GPL / GPL-3.0-only

Recipe:

/hmftools-sv-prep/meta.yaml

package hmftools-sv-prep

versions:

1.2.3-1,  1.2.3-0,  1.1-1,  1.1-0,  1.0.1-0

depends gridss:

2.13.2 h50ea8bc_3

depends openjdk:

>=8

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-sv-prep

and update with::

   mamba update hmftools-sv-prep

To create a new environment, run:

mamba create --name myenvname hmftools-sv-prep

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-sv-prep:<tag>

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

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