recipe biopet-seattleseqkit

#### Tool - Filter This tool can filter a seattle seq file.

Homepage:

https://github.com/biopet/seattleseqkit

License:

MIT

Recipe:

/biopet-seattleseqkit/meta.yaml

#### Tool - Filter

This tool can filter a seattle seq file. A given bed file will only select variants inside this regions. Filtering on specific fields is also possible.

#### Tool - MergeGenes

This tool can merge gene counts from the filter step into 1 combined matrix. Genes that are not there will be filled with 0.

#### Tool - MultiFilter

This tool can filter a seattle seq file. A given bed file will only select variants inside this regions. Filtering on specific fields is also possible.

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

package biopet-seattleseqkit

(downloads) docker_biopet-seattleseqkit

versions:

0.2-1,  0.2-0,  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-seattleseqkit

and update with::

   mamba update biopet-seattleseqkit

To create a new environment, run:

mamba create --name myenvname biopet-seattleseqkit

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-seattleseqkit:<tag>

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

Notes

biopet-seattleseqkit 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-seattleseqkit'. 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-seattleseqkit -Xms512m -Xmx1g'.

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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/biopet-seattleseqkit/README.html)