recipe quatradis

A set of tools to analyse the output from TraDIS analyses

Homepage:

https://github.com/quadram-institute-bioscience/QuaTradis

License:

GPL3 / GPL-3.0-only

Recipe:

/quatradis/meta.yaml

Links:

doi: 10.1093/bioinformatics/btw022

package quatradis

versions:

1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.0-0,  1.0.2-0,  1.0.1-1,  1.0.1-0,  0.8.3-0,  0.8.2-0, 

1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.0-0,  1.0.2-0,  1.0.1-1,  1.0.1-0,  0.8.3-0,  0.8.2-0,  0.7.0-1,  0.7.0-0,  0.6.2-0,  0.5.4-0,  0.4.9-0,  0.4.5-1,  0.4.5-0,  0.4.4-0,  0.4.2-1,  0.4.2-0,  0.3.4-0

depends biopython:

depends bwa:

depends cython:

depends dendropy:

4.6

depends htslib:

depends libgcc:

>=12

depends matplotlib-base:

depends minimap2:

depends numpy:

depends pandas:

depends pysam:

>=0.18.0

depends python:

>=3.10,<3.11.0a0

depends python-graphviz:

depends python_abi:

3.10.* *_cp310

depends r-base:

depends r-getopt:

depends r-mass:

depends samtools:

depends scipy:

depends seaborn-base:

depends setuptools:

depends smalt:

depends snakemake-minimal:

depends snakeviz:

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 quatradis

and update with::

   mamba update quatradis

To create a new environment, run:

mamba create --name myenvname quatradis

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/quatradis:<tag>

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

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