Package Recipe 'fusion-filter'

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:

0.5.0-4, 0.5.0-3, 0.5.0-2, 0.5.0-1, 0.5.0-0

Depends:

on blast >=2.7.1
on gmap >=2017.10.30
on perl
on perl-carp
on perl-db_file
on perl-json-xs
on perl-perlio-gzip
on perl-set-intervaltree
on perl-uri
on python <3
on samtools
on star >=2.5.4a

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install fusion-filter

to add into an existing workspace instead, run:

pixi add fusion-filter

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install fusion-filter

Alternatively, to install into a new environment, run:

conda create -n envname fusion-filter

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/fusion-filter:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/fusion-filter/README.html)