recipe fusion-filter

FusionFilter provides a common fusion-finding, filtering, and annotation framework for the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).

Homepage:

https://github.com/FusionFilter/FusionFilter

License:

BSD-3-Clause

Recipe:

/fusion-filter/meta.yaml

FusionFilter provides a common fusion-finding, filtering, and annotation framework used by the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). This system is leveraged for preparing a target genome and annotation set for fusion transcript identification, fusion feature annotation, and integrates utilities for filtering likely false-positive fusions. - https://github.com/FusionFilter/FusionFilter/wiki

package fusion-filter

versions:

0.5.0-3,  0.5.0-2,  0.5.0-1,  0.5.0-0

depends blast:

>=2.7.1

depends gmap:

>=2017.10.30

depends perl:

depends perl-carp:

depends perl-db-file:

depends perl-json-xs:

depends perl-perlio-gzip:

depends perl-set-intervaltree:

depends perl-uri:

depends python:

<3

depends samtools:

depends star:

>=2.5.4a

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-filter

and update with::

   mamba update fusion-filter

To create a new environment, run:

mamba create --name myenvname fusion-filter

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-filter:<tag>

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

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