aakashsur/hirise repository overview

⁠HiRise in Docker

HiRise⁠ is a popular Hi-C scaffolding method. This container is available via Docker Hub. For more information, visit the GitHub repository⁠.

⁠Usage

docker pull \
  aakashsur/hirise

docker run \
  --rm \
  --volume $PWD:/root/results \
  --workdir /root/results \
  aakashsur/hirise \
  hirise \
  alignment.bam \
  assembly.fasta

⁠Details

The hirise command has been placed in $PATH. Easiest way to run is to have everything in $PWD, i.e. alignment .bam file and assembly .fasta file. The current local directory then gets mounted to the results directory of the container, which is /root/results. HiRise produces a ton of files so I would recommend hardlinking files into a temp directory, running the container, copying the hirise.srf it generates as the final output, then deleting the runtime directory.

The initial and unmaintained publically available code was found to have code breaking problems including deprecated dependencies, broken file structures, and errors in the code. To be sure, the code was published with the HiRise paper, and wasn't intended to be released as a supported software tool. Here, we fork the repository, make enough changes to have the code run, and then build the contianer around the fixed changes. Given that we don't have initmate knowledge of the code, it is not clear if it works as originally intended. One major change is that we don't use a genomic short read alignment as part of the process. It seems that HiRise when published used Merauder as part of the Meraculous assembler pipeline to close gaps. As this is not directly related to Hi-C scaffolding, I simply commented this section out. There is a dockerfile in the HiRise repository, but it appears to not work currently.

To build from scratch -

docker build \
  -t username/hirise:latest \
  path_to_dockerfile

For running in an HPC setting, where singularity is often the choice of containerization -

singularity pull \
  docker://aakashsur/hirise
  
singularity run \
  --bind $PWD:/root/results \
  --workdir /root/results \
  hirise_latest.sif \
  hirise \
  alignment.bam \
  assembly.fasta