- recipe heliano
HELIANO: A fast and accurate tool for detection of Helitron-like elements
- Homepage:
- License:
GNU General Public License v3.0
- Recipe:
- Links:
doi: 10.1093/nar/gkae679
Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.
- package heliano¶
- Versions:
1.3.1-0,1.2.1-0- Depends:
on bedtools
on biopython
on blast
on cd-hit
on dialign2
on emboss
on genometools-genometools
on hmmer
on mafft
on pybedtools
on python
>=3.9on r-base
>=4.1on r-bedtoolsr
on r-seqinr
on rnabob
- 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 heliano
to add into an existing workspace instead, run:
pixi add heliano
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 heliano
Alternatively, to install into a new environment, run:
conda create -n envname heliano
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/heliano:<tag>
(see heliano/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/heliano/README.html)
