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:

• on openjdk >=8,<9

• on python

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install biopet-validatefastq

to add into an existing workspace instead, run:

pixi add biopet-validatefastq

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install biopet-validatefastq

Alternatively, to install into a new environment, run:

conda create -n envname biopet-validatefastq

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/biopet-validatefastq:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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'.

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