recipe pfam_scan

pfam_scan.pl is a Perl script calling HMMER v3 to search a FASTA file against a library of Pfam HMMs.

Homepage:

http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/

License:

GPL (>= 2)

Recipe:

/pfam_scan/meta.yaml

package pfam_scan

versions:

1.6-4,  1.6-3,  1.6-2,  1.6-1,  1.6-0

depends hmmer:

>=3.0

depends perl:

depends perl-bioperl:

>=1.4

depends perl-ipc-run:

depends perl-moose:

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 pfam_scan

and update with::

   mamba update pfam_scan

To create a new environment, run:

mamba create --name myenvname pfam_scan

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/pfam_scan:<tag>

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

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