recipe quast

Quality Assessment Tool for Genome Assemblies

Homepage:

http://quast.sourceforge.net/

License:

Custom

Recipe:

/quast/meta.yaml

Links:

biotools: quast, doi: 10.1093/bioinformatics/btt086

package quast

versions:

5.3.0-0,  5.2.0-4,  5.2.0-3,  5.2.0-2,  5.2.0-1,  5.2.0-0,  5.0.2-7,  5.0.2-6,  5.0.2-5, 

5.3.0-0,  5.2.0-4,  5.2.0-3,  5.2.0-2,  5.2.0-1,  5.2.0-0,  5.0.2-7,  5.0.2-6,  5.0.2-5,  5.0.2-4,  5.0.2-3,  5.0.2-2,  5.0.2-1,  5.0.2-0,  5.0.1-0,  5.0.0-1,  5.0.0-0,  4.6.3-2,  4.6.3-1,  4.6.3-0,  4.6.1-0,  4.5-1,  4.4-1,  4.4-0,  4.3-2,  4.3-1,  4.1-1,  4.1-0,  3.2-1

depends bedtools:

depends blast:

>=2.16.0,<2.17.0a0

depends bwa:

depends circos:

depends glimmerhmm:

depends joblib:

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends matplotlib-base:

depends minimap2:

>=2.10

depends minimap2:

>=2.28,<3.0a0

depends openjdk:

>=8

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends simplejson:

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 quast

and update with::

   mamba update quast

To create a new environment, run:

mamba create --name myenvname quast

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/quast:<tag>

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

Notes

- GeneMark gene prediction software is disabled due to licensing issues

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