Would it be possible to get convert.sh and its dependencies included in the conda environment/container?

[oneillkza]

Thanks again for making SALSA!

I've been running it through the Docker container from Biocontainers, which autobuilds from the conda environment. This works very well for running SALSA itself, but the convert.sh script to produce a .hic file for final editing of the assembly is not included in that.

Right now I've been having to download convert.sh as well as alignments2txt.py, and edit it to point to the right Java, the right juicer_tools, etc. I even found it necessary to run alignments2txt.py inside the container, so as to find all of its dependencies.

It would be very helpful if it convert.sh could just be installed to /usr/local/bin in the container like the rest of the SALSA executables, with the juicer_tools.jar and any other dependencies also there, so it could just be run standalone.