recipe sga

SGA - String Graph Assembler. SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads.

Homepage:

https://github.com/jts/sga

License:

GPL / GPLv3

Recipe:

/sga/meta.yaml

Links:

biotools: sga

package sga

versions:

0.10.15-8,  0.10.15-7,  0.10.15-6,  0.10.15-5,  0.10.15-4,  0.10.15-3,  0.10.15-2,  0.10.15-1,  0.10.15-0, 

0.10.15-8,  0.10.15-7,  0.10.15-6,  0.10.15-5,  0.10.15-4,  0.10.15-3,  0.10.15-2,  0.10.15-1,  0.10.15-0,  0.10.13-0

depends bamtools:

>=2.5.1,<2.5.2.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends sparsehash:

depends zlib:

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 sga

and update with::

   mamba update sga

To create a new environment, run:

mamba create --name myenvname sga

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/sga:<tag>

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

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Link to this page

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