- recipe pypints
Peak Identifier for Nascent Transcripts Starts (PINTS)
- Homepage:
- Developer docs:
- License:
GPL3 / GPL-3.0-only
- Recipe:
- Links:
- package pypints¶
- Versions:
1.2.1-0,1.2.0-0,1.1.15-0,1.1.14-0,1.1.13-0,1.1.10-0,1.1.9-0,1.1.8-0,1.1.7-0,1.2.1-0,1.2.0-0,1.1.15-0,1.1.14-0,1.1.13-0,1.1.10-0,1.1.9-0,1.1.8-0,1.1.7-0,1.1.6-1,1.1.6-0,1.1.4-0,1.1.3-0,1.1.0-0- Depends:
on bedtools
on biopython
on matplotlib-base
on numpy
on pandas
on pybedtools
on pybigwig
on pysam
on python
on requests
on samtools
on scipy
on statsmodels
on tabix
- 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 pypints
to add into an existing workspace instead, run:
pixi add pypints
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 pypints
Alternatively, to install into a new environment, run:
conda create -n envname pypints
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/pypints:<tag>
(see pypints/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.
Notes¶
The tool provides a set of executable files: `pints_caller` (for peak calling, the main program), `pints_visualizer` (for generating bigwig files from bam files), `pints_normalizer` (for normalizing bigwig files by spikein counts), and `pints_boundary_extender`.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pypints/README.html)
