recipe bohra

Pipeline for analysing Illumina data for microbiological public health.

Homepage:

https://github.com/MDU-PHL/bohra

Documentation:

https://github.com/MDU-PHL/bohra/wiki

License:

GPL3 / GPL-3.0-or-later

Recipe:

/bohra/meta.yaml

package bohra

versions:

2.3.7-0,  2.3.6-0,  2.3.4-0,  2.3.3-0,  2.3.2-0,  2.3.0-0,  2.2.1-0,  2.2.0-0,  1.2.20-0, 

2.3.7-0,  2.3.6-0,  2.3.4-0,  2.3.3-0,  2.3.2-0,  2.3.0-0,  2.2.1-0,  2.2.0-0,  1.2.20-0,  1.2.19-1,  1.2.19-0,  1.2.18-0,  1.2.16-0,  1.2.15-0,  1.2.14-0,  1.2.12-0,  1.2.11-0,  1.2.10-1,  1.2.10-0,  1.2.9-0,  1.2.6-0,  1.2.4-0,  1.2.3-0,  1.2.1-0,  1.1.8-0,  1.1.7-0,  1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.27-0,  1.0.26-0,  1.0.25-0,  1.0.24-0,  1.0.23-0,  1.0.22-0,  1.0.20-1,  1.0.20-0,  1.0.19-0

depends altair:

depends any2fasta:

depends biopython:

1.81.*

depends csvtk:

depends jinja2:

depends nextflow:

22.10.6.*

depends numpy:

1.23.1.*

depends packaging:

depends pandas:

1.0.5.*

depends perl-list-moreutils:

depends perl-svg:

depends perl-text-csv:

depends psutil:

depends pytest:

depends pytest-runner:

depends python:

>=3.8

depends sh:

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 bohra

and update with::

   mamba update bohra

To create a new environment, run:

mamba create --name myenvname bohra

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/bohra:<tag>

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

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