recipe linkedsv

A novel structural variant caller for 10X Genomics (linked-read) sequencing data

Homepage:

https://github.com/WGLab/LinkedSV

License:

MIT / MIT

Recipe:

/linkedsv/meta.yaml

package linkedsv

versions:

0.1.0-0

depends bedtools:

depends fermikit:

depends htslib:

>=1.21,<1.22.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends numpy:

depends pandas:

depends perl:

depends pigz:

depends psutil:

depends samtools:

depends scikit-learn:

depends scipy:

depends seaborn:

requirements:

additional platforms:

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 linkedsv

and update with::

   mamba update linkedsv

To create a new environment, run:

mamba create --name myenvname linkedsv

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/linkedsv:<tag>

(see `linkedsv/tags`_ for valid values for ``<tag>``)

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Link to this page

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