recipe fusion-inspector

FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). FusionInspector assists in fusion transcript discovery by performing a supervised analysis of fusion predictions, attempting to recover and re-score evidence for such predictions. - https://github.com/FusionInspector/FusionInspector/wiki

Homepage:

https://github.com/FusionInspector/FusionInspector

License:

BSD-3-Clause

Recipe:

/fusion-inspector/meta.yaml

package fusion-inspector

versions:

2.8.0-0,  2.2.1-0,  1.3.1-1,  1.3.1-0,  1.2.0-0,  1.1.0-2,  1.1.0-1,  1.1.0-0

depends bzip2:

depends gmap:

>=2017.11.15

depends htslib:

>=1.18,<1.19.0a0

depends perl:

depends perl-db-file:

depends perl-set-intervaltree:

depends perl-uri:

depends python:

>=3

depends requests:

>=2.19.1

depends samtools:

>=1.3

depends star:

>=2.6.1b

depends trinity:

>=2.4

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 fusion-inspector

and update with::

   mamba update fusion-inspector

To create a new environment, run:

mamba create --name myenvname fusion-inspector

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/fusion-inspector:<tag>

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

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