recipe fastq-screen

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Homepage:

https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen

Developer docs:

https://github.com/StevenWingett/FastQ-Screen

License:

GPL3 / GPL-3.0-or-later

Recipe:

/fastq-screen/meta.yaml

package fastq-screen

versions:

0.16.0-0,  0.15.3-0,  0.15.2-0,  0.14.0-2,  0.14.0-1,  0.14.0-0,  0.13.0-1,  0.13.0-0,  0.11.3-1, 

0.16.0-0,  0.15.3-0,  0.15.2-0,  0.14.0-2,  0.14.0-1,  0.14.0-0,  0.13.0-1,  0.13.0-0,  0.11.3-1,  0.11.3-0,  0.11.1-1,  0.11.1-0,  0.5.2-1,  0.5.2-0

depends bowtie:

depends bowtie2:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-gdgraph:

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 fastq-screen

and update with::

   mamba update fastq-screen

To create a new environment, run:

mamba create --name myenvname fastq-screen

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/fastq-screen:<tag>

(see `fastq-screen/tags`_ for valid values for ``<tag>``)

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