recipe coltron

Transcriptional regulatory network analysis from ROSE enhancer tables.

Homepage:

BradnerLab/pipeline

Documentation:

https://pypi.org/project/coltron

License:

MIT / MIT

Recipe:

/coltron/meta.yaml

Coltron builds transcriptional regulatory networks from ROSE enhancer tables, BAM signal and motif scans. The upstream 1.0.2 release was written for Python 2 and hard-coded legacy genome paths. This recipe applies a Python 3 compatibility patch and adds command-line options for custom annotation, TF-list and genome FASTA directories, enabling custom genomes such as hg38/GRCh38 when appropriate reference files are supplied.

package coltron#

(downloads) docker_coltron

Versions:

1.0.2-0

Depends:

  • on meme

  • on networkx >=2

  • on numpy

  • on python >=3.10

  • on samtools

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 coltron

to add into an existing workspace instead, run:

pixi add coltron

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 coltron

Alternatively, to install into a new environment, run:

conda create -n envname coltron

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/coltron:<tag>

(see coltron/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page#

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/coltron/README.html)