recipe agat

Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.

Homepage:

https://github.com/NBISweden/AGAT

Documentation:

https://agat.readthedocs.io/en/latest/

License:

GPL / GPLv3

Recipe:

/agat/meta.yaml

AGAT has the power to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised GTF/GFF formats. Over the years it has been enriched by many many tools to perform just about any tasks that is possible related to GTF/GFF format files (sanitizing, conversions, merging, modifying, filtering, FASTA sequence extraction, adding information, etc). Comparing to other methods AGAT is robust to even the most despicable GTF/GFF files.

package agat

versions:

1.4.1-0,  1.4.0-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.0-1,  1.1.0-0, 

1.4.1-0,  1.4.0-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.0-1,  1.0.0-0,  0.9.2-2,  0.9.2-1,  0.9.2-0,  0.9.1-0,  0.9.0-0,  0.8.1-1,  0.8.1-0,  0.8.0-0,  0.6.2-0,  0.6.1-0,  0.6.0-0,  0.5.1-0,  0.5.0-0,  0.4.0-0,  0.3.0-0,  0.2.3-1,  0.2.3-0,  0.2.2-0,  0.2.1-0,  0.1.1-0,  0.1.0-0,  0.0.3-1,  0.0.3-0,  0.0.1-0

depends libdb:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-bioperl-core:

>=1.7.8

depends perl-carp:

depends perl-clone:

depends perl-file-share:

depends perl-file-sharedir-install:

depends perl-graph:

depends perl-list-moreutils:

depends perl-lwp-protocol-https:

depends perl-lwp-simple:

>=6.39

depends perl-moose:

depends perl-sort-naturally:

depends perl-statistics-r:

depends perl-term-progressbar:

depends perl-yaml:

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 agat

and update with::

   mamba update agat

To create a new environment, run:

mamba create --name myenvname agat

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/agat:<tag>

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

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