- recipe star-fusion
STAR-Fusion fusion variant caller. All dependencies required to run FusionInspector and FusionAnnotator are included.
- Homepage:
- Documentation:
- License:
BSD / BSD-3-Clause
- Recipe:
- Links:
doi: 10.1186/s13059-019-1842-9, biotools: star-fusion, usegalaxy-eu: star_fusion
- package star-fusion¶
- Versions:
1.15.1-1,1.15.1-0,1.15.0-0,1.14.0-2,1.14.0-1,1.14.0-0,1.13.0-1,1.13.0-0,1.12.0-1,1.15.1-1,1.15.1-0,1.15.0-0,1.14.0-2,1.14.0-1,1.14.0-0,1.13.0-1,1.13.0-0,1.12.0-1,1.12.0-0,1.11.1-0,1.10.0-1,1.10.0-0,1.9.1-1,1.9.1-0,1.9.0-1,1.9.0-0,1.8.1-2,1.8.1-1,1.8.1-0,1.7.0-1,1.7.0-0,1.6.0-1,1.6.0-0,1.5.0-0,1.4.0-2,1.4.0-1,1.4.0-0,1.3.2-2,1.3.2-1,1.3.2-0,1.2.0-0,1.1.0-0,1.0.0-0,0.7.0-1,0.7.0-0,0.5.4-2,0.5.4-1,0.5.4-0,0.5.3-0,0.4.0-0- Depends:
on bbmap
on blast
on bzip2
on gmap
on htslib
on igv-reports
on openssl
on perl
on perl-carp
on perl-carp-assert
on perl-db_file
on perl-json-xs
on perl-perlio-gzip
on perl-set-intervaltree
on perl-uri
on python
on samtools
<1.10on star
2.7.11bon trinity
<2.9
- 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 star-fusion
to add into an existing workspace instead, run:
pixi add star-fusion
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 star-fusion
Alternatively, to install into a new environment, run:
conda create -n envname star-fusion
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/star-fusion:<tag>
(see star-fusion/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:
[](http://bioconda.github.io/recipes/star-fusion/README.html)
