- recipe haplotype-lso
Haplotype Candidatus Liberibacter solanacearum (Lso) samples from targeted amplicon capillary sequencing data
- Homepage:
- License:
MIT / MIT
- Recipe:
- package haplotype-lso¶
- Versions:
0.4.4-4,0.4.4-3,0.4.4-2,0.4.4-1,0.4.4-0,0.4.3-0,0.4.2-0,0.4.1-0,0.4.0-0,0.4.4-4,0.4.4-3,0.4.4-2,0.4.4-1,0.4.4-0,0.4.3-0,0.4.2-0,0.4.1-0,0.4.0-0,0.3.4-0,0.3.3-0,0.3.2-0,0.3.1-0,0.3.0-0- Depends:
on attrs
on bioconvert
on biopython
>=1.75on blast
on dash
>=1.0on dash-bootstrap-components
on dash-core-components
on dash-html-components
on dash-renderer
on dash-table
on flask
on logzero
on matplotlib-base
on numpy
on pandas
on plotly
on python
on scipy
on seqtk
on xlsxwriter
- 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 haplotype-lso
to add into an existing workspace instead, run:
pixi add haplotype-lso
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 haplotype-lso
Alternatively, to install into a new environment, run:
conda create -n envname haplotype-lso
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/haplotype-lso:<tag>
(see haplotype-lso/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/haplotype-lso/README.html)
