recipe ariba

ARIBA: Antibiotic Resistance Identification By Assembly

Homepage:

https://github.com/sanger-pathogens/ariba

License:

GPL / GNU General Public License v3 (GPL-3.0)

Recipe:

/ariba/meta.yaml

package ariba

versions:

2.14.6-6,  2.14.6-5,  2.14.6-4,  2.14.6-3,  2.14.6-2,  2.14.6-0,  2.14.5-2,  2.14.5-1,  2.14.5-0, 

2.14.6-6,  2.14.6-5,  2.14.6-4,  2.14.6-3,  2.14.6-2,  2.14.6-0,  2.14.5-2,  2.14.5-1,  2.14.5-0,  2.14.4-0,  2.14.3-1,  2.14.3-0,  2.14.1-0,  2.13.5-0,  2.13.3-0,  2.13.2-0,  2.12.1-0,  2.12.0-2,  2.12.0-0,  2.11.1-0,  2.11.0-0,  2.10.1-0,  2.10.0-0,  2.5.1-0,  0.6.0-0

depends bcftools:

>=1.2,<=1.14

depends beautifulsoup4:

>=4.1.0

depends biopython:

depends bowtie2:

<2.4.0

depends cd-hit:

>=4.6.5

depends dendropy:

>=4.2.0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends matplotlib-base:

>=3.1.0

depends mummer:

>=3.23

depends pyfastaq:

>=3.12.0

depends pymummer:

>=0.11.0

depends pysam:

>=0.15.3,<=0.18.0

depends python:

>=3.8,<3.9.0a0

depends python_abi:

3.8.* *_cp38

depends samtools:

>=1.2

depends spades:

>=3.5.0

depends wget:

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 ariba

and update with::

   mamba update ariba

To create a new environment, run:

mamba create --name myenvname ariba

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/ariba:<tag>

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

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