- recipe agat
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
- Homepage:
- Documentation:
- License:
GPL / GPLv3
- Recipe:
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:
1.6.1-1,1.6.1-0,1.5.1-0,1.5.0-0,1.4.2-2,1.4.2-1,1.4.2-0,1.4.1-0,1.4.0-0,1.6.1-1,1.6.1-0,1.5.1-0,1.5.0-0,1.4.2-2,1.4.2-1,1.4.2-0,1.4.1-0,1.4.0-0,1.3.3-0,1.3.2-0,1.3.1-0,1.3.0-0,1.2.0-0,1.1.0-1,1.1.0-0,1.0.0-1,1.0.0-0,0.9.2-2,0.9.2-1,0.9.2-0,0.9.1-0,0.9.0-0,0.8.1-1,0.8.1-0,0.8.0-0,0.6.2-0,0.6.1-0,0.6.0-0,0.5.1-0,0.5.0-0,0.4.0-0,0.3.0-0,0.2.3-1,0.2.3-0,0.2.2-0,0.2.1-0,0.1.1-0,0.1.0-0,0.0.3-1,0.0.3-0,0.0.1-0- Depends:
on libdb
on perl
>=5.32.1,<6.0a0 *_perl5on perl-bioperl-core
>=1.7.8on perl-carp
on perl-clone
on perl-file-chdir
on perl-file-share
on perl-file-sharedir-install
on perl-graph
on perl-ipc-sharelite
on perl-libwww-perl
>=6.39on perl-list-moreutils
on perl-lwp-protocol-https
on perl-moose
on perl-parallel-forkmanager
on perl-sort-naturally
on perl-statistics-r
on perl-term-progressbar
on perl-yaml
on samtools
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install agat
to add into an existing workspace instead, run:
pixi add agat
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install agat
Alternatively, to install into a new environment, run:
conda create -n envname agat
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/agat:<tag>
(see agat/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/agat/README.html)
