recipe stringdecomposer

A tool for decomposing of strings into a set of given monomers

Homepage:

https://github.com/ablab/stringdecomposer

License:

GPL / GPLv2

Recipe:

/stringdecomposer/meta.yaml

StringDecomposer (SD) algorithm takes the set of monomers and a long error-prone read (or a genomic segment) and partitions this read into distinct monomers.

package stringdecomposer

versions:

1.1.2-2,  1.1.2-1,  1.1.2-0,  1.1.1-1,  1.1.1-0,  1.1.0-0,  1.0.0-1,  1.0.0-0,  0.1.0-0

depends _openmp_mutex:

>=4.5

depends biopython:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends pandas:

depends python:

>=3.10,<3.11.0a0

depends python-edlib:

depends python_abi:

3.10.* *_cp310

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 stringdecomposer

and update with::

   mamba update stringdecomposer

To create a new environment, run:

mamba create --name myenvname stringdecomposer

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/stringdecomposer:<tag>

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

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