recipe pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data

Homepage:

http://gmt.genome.wustl.edu/packages/pindel/index.html

License:

GPLv3

Recipe:

/pindel/meta.yaml

Links:

biotools: pindel

package pindel

(downloads) docker_pindel

versions:
0.2.5b9-11,  0.2.5b9-10,  0.2.5b9-9,  0.2.5b9-8,  0.2.5b9-7,  0.2.5b9-6,  0.2.5b9-5,  0.2.5b9-4,  0.2.5b9-3, 

0.2.5b9-11,  0.2.5b9-10,  0.2.5b9-9,  0.2.5b9-8,  0.2.5b9-7,  0.2.5b9-6,  0.2.5b9-5,  0.2.5b9-4,  0.2.5b9-3,  0.2.5b9-2,  0.2.5b9-1,  0.2.5b9-0,  0.2.5b8-2

depends htslib:

>=1.20,<1.22.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

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 pindel

and update with::

   mamba update pindel

To create a new environment, run:

mamba create --name myenvname pindel

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/pindel:<tag>

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

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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/pindel/README.html)