Package Recipe 'hiline'

recipe hiline

HiC alignment and classification pipeline.

Homepage:: https://github.com/wtsi-hpag/HiLine
License:: MIT / MIT
Recipe:: /hiline/meta.yaml

This is a HiC short-read alignment pipeline. It will perform an alignment, or read in an external alignment, perform optional duplicate-read marking, perform HiC read classification based on an in-slico restriction digest of reference sequences and finally split the output alignments based on HiC read-type. It can also optionally process and output HiC alignment statistics. Under the hood, it uses bwa mem and samtools to perform and process alignments. It also uses a custom C++ Python extension to perform the in-silico digest (using the Hyperscan (https://github.com/intel/hyperscan) regex library) and subsequent HiC classification.

package hiline¶

Versions:

0.2.4-1, 0.2.4-0, 0.2.2-1, 0.2.2-0, 0.2.1-0, 0.1-0, 0.0.9-3, 0.0.9-2, 0.0.9-1,

0.2.4-1, 0.2.4-0, 0.2.2-1, 0.2.2-0, 0.2.1-0, 0.1-0, 0.0.9-3, 0.0.9-2, 0.0.9-1, 0.0.9-0, 0.0.8-0, 0.0.7-0, 0.0.6-0, 0.0.5-0, 0.0.3-0, 0.0.2-0, 0.0.1-0

Depends:

on biopython >=1.76
on bwa >=0.7.17
on click >=7.0
on gawk >=5.1.0
on libcxx >=12.0.1
on matplotlib-base >=3.2.0
on minimap2 >=2.17
on numpy >=1.22.2,<2.0a0
on pandas >=1.0.1
on pcre >=8.45,<9.0a0
on perl >=5.30.3
on python >=3.9,<3.10.0a0
on python_abi 3.9.* *_cp39
on samtools >=1.10
on seaborn >=0.10.0

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 hiline

to add into an existing workspace instead, run:

pixi add hiline

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 hiline

Alternatively, to install into a new environment, run:

conda create -n envname hiline

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/hiline:<tag>

(see hiline/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:

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