recipe rrikindp

Evaluation of thermodynamic and kinetic features of RNA-RNA interactions.

Homepage:

https://github.com/mwaldl/RRIkinDP

Documentation:

https://doi.org/10.1101/2023.07.28.548983

License:

GPL / GPL-3.0-only

Recipe:

/rrikindp/meta.yaml

RRIkinDP evaluated thermodynamic and kinetic features of RNA-RNA interactions. As input, two RNA sequences as well as their interaction structure is provided. The tool generates the state space of all intermediate interactions from single base pair interactions to the full input interaction. On top of this state space it computes the barrier energy for the best direct path from a given start interaction to the full input interaction.

package rrikindp

(downloads) docker_rrikindp

versions:

0.0.2-0,  0.0.1-0

depends _openmp_mutex:

* *_llvm

depends _openmp_mutex:

>=4.5

depends boost-cpp:

>=1.78.0,<1.78.1.0a0

depends intarna:

>=3.4.0,<3.5.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends llvm-openmp:

>=17.0.6

depends matplotlib-base:

>=3.7.0

depends pandas:

>=2.0.0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends seaborn:

>=0.12.0

depends viennarna:

>=2.6.0

depends viennarna:

>=2.6.4,<2.7.0a0

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 rrikindp

and update with::

   mamba update rrikindp

To create a new environment, run:

mamba create --name myenvname rrikindp

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/rrikindp:<tag>

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

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