recipe biotradis

A set of tools to analyse the output from TraDIS analyses

Homepage:

https://github.com/sanger-pathogens/Bio-Tradis

License:

GPL3 / GPL-3.0-only

Recipe:

/biotradis/meta.yaml

package biotradis

versions:

1.4.5-5,  1.4.5-4,  1.4.5-3,  1.4.5-2,  1.4.5-1,  1.4.5-0,  1.4.1-0,  1.4.1.dev-4,  1.4.1.dev-3, 

1.4.5-5,  1.4.5-4,  1.4.5-3,  1.4.5-2,  1.4.5-1,  1.4.5-0,  1.4.1-0,  1.4.1.dev-4,  1.4.1.dev-3,  1.4.1.dev-2,  1.4.1.dev-1,  1.4.1.dev-0

depends bioconductor-edger:

depends bwa:

depends htslib:

depends perl:

depends perl-app-cpanminus:

depends perl-bioperl:

>=1.7.2

depends perl-exception-class:

depends perl-local-lib:

depends perl-moose:

depends perl-parallel-forkmanager:

depends perl-pathtools:

depends perl-scalar-util-numeric:

depends perl-text-csv:

depends r-base:

depends r-getopt:

depends r-mass:

depends samtools:

depends smalt:

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 biotradis

and update with::

   mamba update biotradis

To create a new environment, run:

mamba create --name myenvname biotradis

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/biotradis:<tag>

(see `biotradis/tags`_ for valid values for ``<tag>``)

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