recipe gmap-fusion

GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.

Homepage:

https://github.com/GMAP-fusion/GMAP-fusion

License:

BSD-3-Clause

Recipe:

/gmap-fusion/meta.yaml

package gmap-fusion

versions:

0.4.0-2,  0.4.0-0,  0.3.0-1

depends bowtie2:

>=2.1

depends gmap:

>=2017.11.15

depends perl:

depends perl-db-file:

depends perl-set-intervaltree:

depends samtools:

>=1.3

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 gmap-fusion

and update with::

   mamba update gmap-fusion

To create a new environment, run:

mamba create --name myenvname gmap-fusion

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/gmap-fusion:<tag>

(see `gmap-fusion/tags`_ for valid values for ``<tag>``)

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Link to this page

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