recipe repeatmodeler

RepeatModeler is a de-novo repeat family identification and modeling package.

Homepage:

https://www.repeatmasker.org/RepeatModeler/

Developer docs:

https://github.com/Dfam-consortium/RepeatModeler

License:

Open Software License v2.1

Recipe:

/repeatmodeler/meta.yaml

Links:

biotools: RepeatModeler

package repeatmodeler

versions:

2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2a-1,  2.0.2a-0,  2.0.1-0,  1.0.11-3,  1.0.11-2,  1.0.11-1, 

2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2a-1,  2.0.2a-0,  2.0.1-0,  1.0.11-3,  1.0.11-2,  1.0.11-1,  1.0.11-0,  1.0.8-1,  1.0.8-0

depends cd-hit:

>=4.8.1

depends genometools-genometools:

>=1.6

depends ltr_retriever:

>=2.9

depends mafft:

>=7.471

depends ninja-nj:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-devel-size:

depends perl-file-which:

depends perl-libwww-perl:

depends perl-uri:

depends recon:

>=1.08

depends repeatmasker:

>=4.1.5

depends repeatscout:

>=1.0.6

depends rmblast:

>=2.13.0

depends trf:

>=4.09

depends ucsc-fatotwobit:

depends ucsc-twobitinfo:

depends ucsc-twobittofa:

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 repeatmodeler

and update with::

   mamba update repeatmodeler

To create a new environment, run:

mamba create --name myenvname repeatmodeler

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/repeatmodeler:<tag>

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

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