recipe biopet-validatevcf

ValidateVcf validates a VCF file against a reference genomes.

Homepage:

https://github.com/biopet/validatevcf

License:

MIT

Recipe:

/biopet-validatevcf/meta.yaml

ValidateVcf validates a VCF file against a reference genomes. It checks if the positions present in the VCF are also present on the reference genoome.

For documentation and manuals visit our github.io page: https://biopet.github.io/validatevcf

package biopet-validatevcf

(downloads) docker_biopet-validatevcf

versions:

0.1-1,  0.1-0

depends openjdk:

>=8,<9

depends python:

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 biopet-validatevcf

and update with::

   mamba update biopet-validatevcf

To create a new environment, run:

mamba create --name myenvname biopet-validatevcf

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/biopet-validatevcf:<tag>

(see `biopet-validatevcf/tags`_ for valid values for ``<tag>``)

Notes

biopet-validatevcf is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-validatevcf'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-validatevcf -Xms512m -Xmx1g'.

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