recipe gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.

Homepage:

https://ccb.jhu.edu/software/stringtie/gff.shtml

Documentation:

https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread

Developer docs:

https://github.com/gpertea/gffread

License:

MIT / MIT

Recipe:

/gffread/meta.yaml

Links:

biotools: gffread, usegalaxy-eu: gffread, doi: 10.12688/f1000research.23297.2

package gffread

(downloads) docker_gffread

versions:
0.12.7-6,  0.12.7-5,  0.12.7-4,  0.12.7-3,  0.12.7-2,  0.12.7-1,  0.12.7-0,  0.12.1-1,  0.12.1-0, 

0.12.7-6,  0.12.7-5,  0.12.7-4,  0.12.7-3,  0.12.7-2,  0.12.7-1,  0.12.7-0,  0.12.1-1,  0.12.1-0,  0.11.7-0,  0.11.6-0,  0.11.4-0,  0.9.12-0,  0.9.9-1,  0.9.9-0,  0.9.8-0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 gffread

and update with::

   mamba update gffread

To create a new environment, run:

mamba create --name myenvname gffread

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/gffread:<tag>

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

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Link to this page

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