recipe extract-sv-reads

Tool for extracting splitter or discordant reads from a BAM or CRAM file.

Homepage:

https://github.com/hall-lab/extract_sv_reads

License:

MIT

Recipe:

/extract-sv-reads/meta.yaml

package extract-sv-reads

versions:

1.3.0-5,  1.3.0-4,  1.3.0-3,  1.3.0-2,  1.3.0-1,  1.3.0-0,  1.2.1-1,  1.2.1-0,  1.1.2-0, 

1.3.0-5,  1.3.0-4,  1.3.0-3,  1.3.0-2,  1.3.0-1,  1.3.0-0,  1.2.1-1,  1.2.1-0,  1.1.2-0,  1.1.0-0

depends boost-cpp:

depends htslib:

1.9.*

depends htslib:

>=1.9,<1.10.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

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 extract-sv-reads

and update with::

   mamba update extract-sv-reads

To create a new environment, run:

mamba create --name myenvname extract-sv-reads

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/extract-sv-reads:<tag>

(see `extract-sv-reads/tags`_ for valid values for ``<tag>``)

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