recipe biopet-extractadaptersfastqc

ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report.

Homepage:

https://github.com/biopet/extractadaptersfastqc

License:

MIT

Recipe:

/biopet-extractadaptersfastqc/meta.yaml

ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report. These sequences can be used as input for a QC tool such as cutadapt. The sequences can be output in plain text format with a newline character as a separator between the sequences. Alternatively the sequences can be output in FASTA format. For documentation and manuals visit our github.io page: https://biopet.github.io/extractadaptersfastqc

package biopet-extractadaptersfastqc

(downloads) docker_biopet-extractadaptersfastqc

versions:

0.2-3,  0.2-2,  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-extractadaptersfastqc

and update with::

   mamba update biopet-extractadaptersfastqc

To create a new environment, run:

mamba create --name myenvname biopet-extractadaptersfastqc

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-extractadaptersfastqc:<tag>

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

Notes

biopet-extractadaptersfastqc 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-extractadaptersfastqc'. 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-extractadaptersfastqc -Xms512m -Xmx1g'.

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