recipe stringtie

StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome.

Homepage:

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

Documentation:

https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual

Developer docs:

https://github.com/gpertea/stringtie

License:

MIT / MIT

Recipe:

/stringtie/meta.yaml

Links:

biotools: stringtie, usegalaxy-eu: stringtie, doi: 10.1038/nbt.3122, doi: 10.1038/nprot.2016.095, doi: 10.1186/s13059-019-1910-1

package stringtie

versions:

2.2.3-0,  2.2.2-0,  2.2.1-6,  2.2.1-4,  2.2.1-3,  2.2.1-2,  2.2.1-1,  2.2.1-0,  2.2.0-1, 

2.2.3-0,  2.2.2-0,  2.2.1-6,  2.2.1-4,  2.2.1-3,  2.2.1-2,  2.2.1-1,  2.2.1-0,  2.2.0-1,  2.2.0-0,  2.1.7-0,  2.1.6-0,  2.1.5-1,  2.1.5-0,  2.1.4-0,  2.1.2-1,  2.1.2-0,  2.1.1-0,  2.0-0,  1.3.6-0,  1.3.5-0,  1.3.4-1,  1.3.4-0,  1.3.3-4,  1.3.3-3,  1.3.3-2,  1.3.3b-1,  1.3.3b-0,  1.3.0-2,  1.3.0-1,  1.3.0-0,  1.2.4-2,  1.2.4-1,  1.2.4-0,  1.2.3-0,  1.2.2-2,  1.2.2-1,  1.2.0-1,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.4-1,  1.0.4-0,  1.0.3-1,  1.0.3-0,  1.0.1-0,  0.97-0

depends htslib:

>=1.20,<1.22.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends python:

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 stringtie

and update with::

   mamba update stringtie

To create a new environment, run:

mamba create --name myenvname stringtie

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/stringtie:<tag>

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

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