recipe lumpy-sv

a general probabilistic framework for structural variant discovery

Homepage:

https://github.com/arq5x/lumpy-sv

License:

MIT

Recipe:

/lumpy-sv/meta.yaml

package lumpy-sv

versions:

0.3.1-3,  0.3.1-2,  0.3.1-1,  0.3.1-0,  0.3.0-6,  0.3.0-5,  0.3.0-4,  0.3.0-3,  0.3.0-2, 

0.3.1-3,  0.3.1-2,  0.3.1-1,  0.3.1-0,  0.3.0-6,  0.3.0-5,  0.3.0-4,  0.3.0-3,  0.3.0-2,  0.3.0-1,  0.3.0-0,  0.2.14a-2,  0.2.14a-1,  0.2.14a-0,  0.2.13-1,  0.2.13-0,  0.2.12-3,  0.2.12-2,  0.2.12-1,  0.2.12-0,  0.2.11-0

depends bamkit:

depends gawk:

depends htslib:

depends lumpy-sv-minimal:

0.3.1.*

depends numpy:

depends pysam:

depends python:

2.7.*

depends sambamba:

depends samblaster:

depends samtools:

depends util-linux:

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 lumpy-sv

and update with::

   mamba update lumpy-sv

To create a new environment, run:

mamba create --name myenvname lumpy-sv

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/lumpy-sv:<tag>

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

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