recipe star-fusion

STAR-Fusion fusion variant caller. All dependencies required to run FusionInspector and FusionAnnotator are included.

Homepage:

https://github.com/STAR-Fusion/STAR-Fusion

Documentation:

https://github.com/STAR-Fusion/STAR-Fusion/wiki

License:

BSD / BSD-3-Clause

Recipe:

/star-fusion/meta.yaml

Links:

doi: 10.1186/s13059-019-1842-9, biotools: star-fusion, usegalaxy-eu: star_fusion

package star-fusion

(downloads) docker_star-fusion

versions:
1.13.0-01.12.0-11.12.0-01.11.1-01.10.0-11.10.0-01.9.1-11.9.1-01.9.0-1

1.13.0-01.12.0-11.12.0-01.11.1-01.10.0-11.10.0-01.9.1-11.9.1-01.9.0-11.9.0-01.8.1-21.8.1-11.8.1-01.7.0-11.7.0-01.6.0-11.6.0-01.5.0-01.4.0-21.4.0-11.4.0-01.3.2-21.3.2-11.3.2-01.2.0-01.1.0-01.0.0-00.7.0-10.7.0-00.5.4-20.5.4-10.5.4-00.5.3-00.4.0-0

depends bbmap:

depends blast:

depends bzip2:

depends gmap:

depends htslib:

depends igv-reports:

depends openssl:

depends perl:

depends perl-carp:

depends perl-carp-assert:

depends perl-db-file:

depends perl-io-gzip:

depends perl-json-xs:

depends perl-set-intervaltree:

depends perl-uri:

depends python:

depends samtools:

<1.10

depends star:

2.7.8a

depends trinity:

<2.9

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 star-fusion

and update with::

   mamba update star-fusion

To create a new environment, run:

mamba create --name myenvname star-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/star-fusion:<tag>

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

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