recipe tb-profiler

Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data

Homepage:

https://github.com/jodyphelan/TBProfiler

License:

GPL3 / GPL-3.0-or-later

Recipe:

/tb-profiler/meta.yaml

Links:

doi: 10.1186/s13073-019-0650-x

package tb-profiler

versions:

6.2.0-0,  6.1.0-1,  6.1.0-0,  6.0.0-0,  5.0.1-1,  5.0.1-0,  5.0.0-0,  4.4.2-0,  4.4.1-0, 

6.2.0-0,  6.1.0-1,  6.1.0-0,  6.0.0-0,  5.0.1-1,  5.0.1-0,  5.0.0-0,  4.4.2-0,  4.4.1-0,  4.4.0-0,  4.3.0-0,  4.2.0-0,  4.1.1-1,  4.1.1-0,  4.1.0-0,  4.0.3-0,  4.0.2-1,  4.0.2-0,  4.0.1-0,  4.0.0-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.5-0,  3.0.4-0,  3.0.3-0,  3.0.2-0,  3.0.1-0,  3.0.0-0,  2.8.14-0,  2.8.13-0,  2.8.12-2,  2.8.12-1,  2.8.12-0,  2.8.11-0,  2.8.10-0,  2.8.9-0,  2.8.8-0,  2.8.6-0,  2.8.5-0,  2.8.4-0,  2.8.3-0,  2.8.2-0,  2.8.1-0,  2.8.0-1,  2.8.0-0,  2.7.4-0,  2.7.3-0,  2.7.2-0,  2.7.1-0,  2.7-0,  2.6.1-2,  2.6.1-1,  2.6.1-0,  2.6-0,  2.5-1,  2.5-0,  2.4-0,  2.3-0,  2.2-1,  2.2-0,  2.1-2,  2.1-1,  2.1-0,  2.0-0

depends docxtpl:

depends filelock:

depends git:

depends iqtree:

depends jinja2:

depends joblib:

depends pathogen-profiler:

4.1.0.*

depends pysam:

depends python:

>=3.8

depends rich-argparse:

depends tqdm:

depends usher:

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 tb-profiler

and update with::

   mamba update tb-profiler

To create a new environment, run:

mamba create --name myenvname tb-profiler

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/tb-profiler:<tag>

(see `tb-profiler/tags`_ for valid values for ``<tag>``)

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