recipe biopet-sampleconfig

#### Tools - ExtractTsv This mean can extract samples, libraries and readgroups from a sample config file.

Homepage:

https://github.com/biopet/sampleconfig

License:

MIT

Recipe:

/biopet-sampleconfig/meta.yaml

#### Tools - ExtractTsv

This mean can extract samples, libraries and readgroups from a sample config file. This meant as a supporting tool inside wdl pipelines. It can also output a single layer as tsv file.

#### Tools - ReadFromTsv

This tool enables a user to create a full sample sheet in JSON format or YAML format, suitable for all Biopet Queue pipelines, from TSV file(s).

#### Tools - CromwellArrays

This tool will convert the sample configs to a array based format that can be used inside wdl pipelines. This tool is only to support biowdl pipelines.

#### Tools - CaseControl

This tool will extract the case-control pairs from a sample config file. It will read the headers of the bam files to confirm that samples do exist.

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

package biopet-sampleconfig

(downloads) docker_biopet-sampleconfig

versions:

0.3-1,  0.3-0,  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-sampleconfig

and update with::

   mamba update biopet-sampleconfig

To create a new environment, run:

mamba create --name myenvname biopet-sampleconfig

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-sampleconfig:<tag>

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

Notes

biopet-sampleconfig 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-sampleconfig'. 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-sampleconfig -Xms512m -Xmx1g'.

Download stats

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-sampleconfig/README.html)