recipe sshmm

ssHMM is an RNA motif finder that recovers sequence-structure motifs from RNA-binding protein data, such as CLIP-Seq data.

Homepage:

https://github.molgen.mpg.de/heller/ssHMM

License:

GPL-3.0

Recipe:

/sshmm/meta.yaml

package sshmm

versions:

1.0.7-4,  1.0.7-3,  1.0.7-2,  1.0.7-1,  1.0.7-0

depends bedtools:

depends forgi:

depends ghmm:

depends graphviz:

>=2.40.1,<3.0a0

depends libgcc-ng:

>=9.3.0

depends libxml2:

>=2.9.10,<2.10.0a0

depends numpy:

1.11.*

depends pygraphviz:

depends python:

>=2.7,<2.8.0a0

depends python_abi:

2.7.* *_cp27mu

depends rnashapes:

2.1.6.*

depends rnastructure:

depends weblogo:

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 sshmm

and update with::

   mamba update sshmm

To create a new environment, run:

mamba create --name myenvname sshmm

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/sshmm:<tag>

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

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