recipe antismash-lite

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

Homepage:

https://docs.antismash.secondarymetabolites.org/intro/

Documentation:

https://docs.antismash.secondarymetabolites.org

Developer docs:

https://github.com/antismash/antismash

License:

AGPL / AGPL-3.0-or-later

Recipe:

/antismash-lite/meta.yaml

Links:

biotools: antismash, doi: 10.1093/nar/gkr466, doi: 10.1093/nar/gkt449, doi: 10.1093/nar/gkv437, doi: 10.1093/nar/gkx319, doi: 10.1093/nar/gkz310, doi: 10.1093/nar/gkab335, doi: 10.1093/nar/gkad344, usegalaxy-eu: antismash

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.

package antismash-lite

versions:

7.1.0-0,  6.1.1-1,  6.1.1-0,  6.1.0-0,  6.0.1-1,  6.0.1-0

depends bcbio-gff:

depends biopython:

1.78.*

depends blast:

depends brawn:

>=1.0.1

depends diamond:

depends fasttree:

2.1.*

depends glimmerhmm:

3.0.*

depends helperlibs:

>=0.2.1

depends hmmer:

>=3.1b2

depends hmmer2:

depends jinja2:

depends joblib:

depends jsonschema:

depends libsass:

depends markupsafe:

>=2.1.0

depends matplotlib-base:

depends meme:

4.11.2.*

depends moods:

>=1.9.4

depends nrpys:

>=0.1.1

depends numpy:

depends prodigal:

depends pysvg-py3:

depends python:

>=3.9

depends scikit-learn:

>=1.3.2

depends scipy:

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 antismash-lite

and update with::

   mamba update antismash-lite

To create a new environment, run:

mamba create --name myenvname antismash-lite

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/antismash-lite:<tag>

(see `antismash-lite/tags`_ for valid values for ``<tag>``)

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