Package Recipe 'biopet-validatefastq'

recipe biopet-validatefastq

This tool validates a FASTQ file.

Homepage:: https://github.com/biopet/validatefastq
License:: MIT
Recipe:: /biopet-validatefastq/meta.yaml

This tool validates a FASTQ file. When data is paired it can also validate a pair of FASTQ files. ValidateFastq will check if the FASTQ is in valid FASTQ format. This includes checking for duplicate reads and checking whether a pair of FASTQ files contains the same amount of reads and headers match. It also check whether the quality encodings are correct and outputs the most likely encoding format (Sanger, Solexa etc.).

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

package biopet-validatefastq¶

versions:

0.1.1-3, 0.1.1-2, 0.1.1-1, 0.1.1-0

depends openjdk:

>=8,<9

depends python:

requirements:

additional platforms:

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-validatefastq

and update with::

   mamba update biopet-validatefastq

To create a new environment, run:

mamba create --name myenvname biopet-validatefastq

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-validatefastq:<tag>

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

Notes¶

biopet-validatefastq 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-validatefastq'. 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-validatefastq -Xms512m -Xmx1g'.

Download stats¶

Link to this page¶

Render an 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-validatefastq/README.html)