recipe treesapp

TreeSAPP is a functional and taxonomic annotation tool for microbial genomes and proteins

Homepage:

https://github.com/hallamlab/TreeSAPP

License:

GPL3 / GPL-3.0-only

Recipe:

/treesapp/meta.yaml

package treesapp

versions:

0.11.4-1,  0.11.4-0,  0.11.3-1,  0.11.3-0,  0.11.2-0,  0.11.0-0,  0.10.4-1,  0.10.4-0,  0.10.3-1, 

0.11.4-1,  0.11.4-0,  0.11.3-1,  0.11.3-0,  0.11.2-0,  0.11.0-0,  0.10.4-1,  0.10.4-0,  0.10.3-1,  0.10.3-0,  0.10.2-0,  0.10.1-0,  0.10.0-0,  0.9.8-0,  0.9.7-0,  0.9.6-1,  0.9.6-0,  0.9.5-0,  0.9.2-1,  0.9.2-0,  0.9.1-0,  0.9.0-0,  0.8.9-0,  0.6.8-1,  0.6.8-0,  0.6.7-0,  0.6.6-0,  0.6.5-0

depends biopython:

>=1.78

depends bwa:

>=0.7.17

depends epa-ng:

>=0.3.8

depends ete3:

>=3.1.2

depends fasttree:

>=2.1.10

depends hmmer:

>=3.3

depends joblib:

1.0.0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends mafft:

>=7.471

depends matplotlib-base:

>=3.3.0

depends mmseqs2:

>=12.113e3

depends numpy:

>=1.18.1

depends packaging:

>=20.4

depends pandas:

>=1.1.0

depends prodigal:

>=2.6.2

depends pyfastx:

>=0.8.2

depends pygtrie:

>=2.3.3

depends python:

>=3.6,<3.7.0a0

depends python_abi:

3.6.* *_cp36m

depends raxml-ng:

>=1.0.1

depends samsum:

>=0.1.4

depends scikit-learn:

0.23.1

depends scipy:

>=1.5.2

depends seaborn:

>=0.11.0

depends six:

>=1.15.0

depends tqdm:

>=4.50.0

depends vsearch:

>=2.15.0

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 treesapp

and update with::

   mamba update treesapp

To create a new environment, run:

mamba create --name myenvname treesapp

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/treesapp:<tag>

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

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