recipe rnashapes

RNAshape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space.

Homepage:

https://bibiserv.cebitec.uni-bielefeld.de/rnashapes

License:

GPL-3.0-or-later

Recipe:

/rnashapes/meta.yaml

Links:

doi: 10.1093/bioinformatics/btu649

package rnashapes

(downloads) docker_rnashapes

versions:
3.4.0-2,  3.4.0-1,  3.4.0-0,  3.3.2-3,  3.3.2-2,  3.3.2-1,  3.3.2-0,  3.3.0-7,  3.3.0-6, 

3.4.0-2,  3.4.0-1,  3.4.0-0,  3.3.2-3,  3.3.2-2,  3.3.2-1,  3.3.2-0,  3.3.0-7,  3.3.0-6,  3.3.0-5,  3.3.0-4,  3.3.0-3,  3.3.0-0,  2.1.6-4,  2.1.6-3,  2.1.6-2,  2.1.6-1,  2.1.6-0

depends bellmans-gapc:

>=2024.01.12

depends bellmans-gapc:

>=2024.1.12

depends libgcc:

>=13

depends libopenblas:

>=0.3.28,<1.0a0

depends libstdcxx:

>=13

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

requirements:

additional platforms:
linux-aarch64

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 rnashapes

and update with::

   mamba update rnashapes

To create a new environment, run:

mamba create --name myenvname rnashapes

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/rnashapes:<tag>

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

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