Lachesis was the first Hi-C assembler and is widely cited. However it has not been maintained and is quite challenging to install. Forked from another repo, this repo fleshes out the details to help make a docker container a stand-in exectuable for Lachesis.
docker pull \
aakashsur/lachesis
docker run \
--rm \
--volume $PWD:/root \
aakashsur/lachesis \
lachesis \
/root/configuration.ini
The Lachesis command has been placed in $PATH. Easiest way to run is to have everything in $PWD, i.e. .ini file, sorted .bam file, and assembly .fasta file. The current local directory then gets mounted to the home directory of the container, which is /root/. In your .ini file, make sure your paths are absolute and something to the effect of /root/configuration.ini, /root/assembly.fasta, /root/sorted.bam. I've included a .ini file I was using to test for yeast for good measure.
I haven't bothered installing R which is needed for drawing the heatmaps since I think there are better visualization tools now, but feel free to amend and then build from the Dockerfile if you so choose. Be warned, the build process requies at least 2GB of memory, I know this because I tried builing on an AWS nano instance and got cryptic error messages. Spooky!
docker build \
-t username/lachesis:latest \
path_to_dockerfile
For running in an HPC setting, where singularity is often the choice of containerization -
singularity pull \
docker://aakashsur/lachesis
singularity run \
--bind $PWD:/root \
lachesis_latest.sif \
lachesis \
/root/configuration.ini