recipe islandpath

IslandPath-DIMOB is a standalone software to predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes.

Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest.

Homepage:

http://www.pathogenomics.sfu.ca/islandpath/

License:

GNU General Public License v3.0

Recipe:

/islandpath/meta.yaml

package islandpath

versions:

1.0.6-0,  1.0.5-0,  1.0.4-2,  1.0.4-1,  1.0.4-0,  1.0.3-0

depends hmmer:

depends perl:

depends perl-bioperl:

>=1.7.2

depends perl-config-simple:

depends perl-data-dumper:

depends perl-log-log4perl:

depends perl-moose:

depends perl-moosex-singleton:

requirements:

additional platforms:

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 islandpath

and update with::

   mamba update islandpath

To create a new environment, run:

mamba create --name myenvname islandpath

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/islandpath:<tag>

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

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Link to this page

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