recipe abyss

Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.

Homepage:

https://www.bcgsc.ca/platform/bioinfo/software/abyss

Documentation:

https://github.com/bcgsc/abyss/blob/v2.3.10/README.md

Developer docs:

https://github.com/bcgsc/abyss

License:

GPL3 / GPL-3.0-only

Recipe:

/abyss/meta.yaml

Links:

biotools: abyss, usegalaxy-eu: abyss-pe, doi: 10.1101/gr.214346.116, doi: 10.1101/gr.089532.108

package abyss

versions:

2.3.10-0,  2.3.9-0,  2.3.8-1,  2.3.8-0,  2.3.7-4,  2.3.7-3,  2.3.7-2,  2.3.7-1,  2.3.7-0, 

2.3.10-0,  2.3.9-0,  2.3.8-1,  2.3.8-0,  2.3.7-4,  2.3.7-3,  2.3.7-2,  2.3.7-1,  2.3.7-0,  2.3.6-1,  2.3.6-0,  2.3.5-1,  2.3.5-0,  2.3.4-1,  2.3.4-0,  2.3.3-1,  2.3.3-0,  2.3.2-0,  2.3.1-0,  2.3.0-0,  2.2.5-1,  2.2.5-0,  2.2.4-0,  2.2.3-2,  2.2.3-1,  2.2.3-0,  2.2.2-0,  2.2.1-0,  2.1.5-1,  2.1.5-0,  2.1.4-0,  2.1.3-0,  2.1.1-0,  2.1.0-0,  2.0.2-5,  2.0.2-4,  2.0.2-3,  2.0.2-2,  2.0.2-1,  2.0.2-0,  2.0.1-2,  2.0.1-1,  2.0.1-0,  1.9.0-7,  1.9.0-6,  1.9.0-5,  1.9.0-4,  1.9.0-3,  1.9.0-2,  1.9.0-1,  1.9.0-0,  1.5.2-5,  1.5.2-4,  1.5.2-3,  1.5.2-2,  1.5.2-1,  1.5.2-0

depends boost-cpp:

depends btllib:

>=1.7.3,<2.0a0

depends libgcc:

>=12

depends libstdcxx:

>=12

depends make:

depends openmpi:

>=4.1.6,<5.0a0

depends perl:

depends util-linux:

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 abyss

and update with::

   mamba update abyss

To create a new environment, run:

mamba create --name myenvname abyss

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/abyss:<tag>

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

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