Blazing fast toolkit to work with .hic and .cool files
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This repository hosts the Docker images for hictk: a blazing fast toolkit to work with .hic and .cool files.
hictk is developed and maintained by the Paulsen group.
If you have questions regarding hictk, please start a new discussion on GitHub.
Docker images are automatically built via GitHub Actions when a commit is pushed to the main branch or when a new release is tagged.
Build logs: link
Dockerfile linksThis image contains the hictk CLI tools, which consist of a single binary (hictk) with several subcommands.
First, pull the latest version of hictk from DockerHub.
For production use, we recommend pulling the latest stable release:
docker pull paulsengroup/hictk:2.2.0
Otherwise, feel free to pull the latest available image:
docker pull paulsengroup/hictk
Note that depending on your OS, you may need admin/root permissions (which are usually obtained by e.g. prefixing the pull command with sudo).
user@dev:/tmp$ docker run paulsengroup/hictk:2.2.0 --help
Blazing fast tools to work with .hic and .cool files.
/usr/local/bin/hictk [OPTIONS] [SUBCOMMANDS]
OPTIONS:
-h, --help Print this help message and exit
-V, --version Display program version information and exit
[Option Group: help]
[At most 1 of the following options are allowed]
OPTIONS:
--help-cite Print hictk's citation in Bibtex format and exit.
--help-build-meta Print information regarding hictk's build options and third-party
dependencies, and exit.
--help-docs Print the URL to hictk's documentation and exit.
--help-license Print the hictk license and exit.
--help-telemetry Print information regarding telemetry collection and exit.
SUBCOMMANDS:
balance Balance Hi-C files using ICE, SCALE, or VC.
convert Convert Hi-C files between different formats.
dump Read interactions and other kinds of data from .hic and Cooler
files and write them to stdout.
fix-mcool Fix corrupted .mcool files.
load Build .cool and .hic files from interactions in various text
formats.
merge Merge multiple Cooler or .hic files into a single file.
metadata Print file metadata to stdout.
rename-chromosomes, rename-chromsRename chromosomes found in Cooler files.
validate Validate .hic and Cooler files.
zoomify Convert single-resolution Cooler and .hic files to
multi-resolution by coarsening.
For more details and examples on how to use hictk, please refer to the official documentation.
If you use hictk in your research, please cite the following publication:
Roberto Rossini, Jonas Paulsen, hictk: blazing fast toolkit to work with .hic and .cool files Bioinformatics, Volume 40, Issue 7, July 2024, btae408, https://doi.org/10.1093/bioinformatics/btae408
@article{hictk,
author = {Rossini, Roberto and Paulsen, Jonas},
title = "{hictk: blazing fast toolkit to work with .hic and .cool files}",
journal = {Bioinformatics},
volume = {40},
number = {7},
pages = {btae408},
year = {2024},
month = {06},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btae408},
url = {https://doi.org/10.1093/bioinformatics/btae408},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/40/7/btae408/58385157/btae408.pdf},
}
hictk itself is released under the MIT License.
However, the hictk Docker image is based on one of the official Ubuntu images (currently 24.04), which contains software that may be released under a different license.
For more details, please refer to the README of the official Ubuntu image on DockerHub: link.
Content type
Image
Digest
sha256:addc13ede…
Size
37.2 MB
Last updated
6 months ago
Requires Docker Desktop 4.37.1 or later.
Pulls:
87
Last week