Installation

Conda (bioconda)

The hictk package for Linux and macOS is available on bioconda and can be installed as follows:

user@dev:/tmp$ conda create -n hictk -c conda-forge -c bioconda hictk

user@dev:/tmp$ conda activate hictk

(hictk) user@dev:/tmp$ whereis hictk
hictk: /home/user/.miniconda3/envs/hictk/bin/hictk

(hictk) user@dev:/tmp$ hictk --version
hictk-v2.2.0-bioconda

Containers (Docker or Singularity/Apptainer)

First, ensure you have followed the instructions on how to install Docker or Singularity/Apptainer on your OS.

Installing Docker

The following instructions assume you have root/admin permissions.

• Linux

• macOS

• Windows

On some Linux distributions, simply installing Docker is not enough. You also need to start (and optionally enable) the appropriate service(s). This is usually done with one of the following:

sudo systemctl start docker
sudo systemctl start docker.service

Refer to Docker or your OS/distribution documentation for more details.

Pulling hictk Docker image

hictk Docker images are available on GHCR.io and DockerHub.

Downloading and running the latest stable release can be done as follows:

# Using Docker, may require sudo
user@dev:/tmp$ docker run ghcr.io/paulsengroup/hictk:2.2.0 --help

# Using Singularity/Apptainer
user@dev:/tmp$ singularity run ghcr.io/paulsengroup/hictk:2.2.0 --help

Blazing fast tools to work with .hic and .cool files.
Usage: hictk [OPTIONS] SUBCOMMAND
Options:
  -h,--help                   Print this help message and exit
  -V,--version                Display program version information 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-chroms
                              Rename chromosomes found in Cooler files.
  validate                    Validate .hic and Cooler files.
  zoomify                     Convert single-resolution Cooler and .hic files to multi-resolution by coarsening.

The above will print hictk’s help message, and is equivalent to running hictk --help from the command line (assuming hictk is available on your machine).

Installing from source

Please refer to hictk’s build instructions.