update singularity support#113
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owlang wants to merge 2 commits intoay-lab:masterfrom
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Since there are several issue tickets indicating problems with container-based use (ay-lab#112, ay-lab#106, ay-lab#94, ay-lab#88, ay-lab#85), it may be helpful to users for the documentation to be updated accordingly. Not sure how docs are hosted but this may also need a redeployment after PR.
- adding .def file for building a singularity container with FitHiChIP + all dependencies set up inside the image built from this (see help for usage, different from FitHiChIP_Singularity.sh) - removed old Singularity to avoid confusion - can always check history to bring it back
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This is an alternative way of using singularity containers - not compatible with the bash wrapper (
FitHiChIP_Singularity.sh).When
singularity.defis built, the resulting image should have FitHiChIP (v 11.0) + all dependencies set up inside. See %help for details and usesingularity run-helpfor usage (different fromFitHiChIP_Singularity.sh).Some notes:
whichb/c of the way FitHiChIP_HiCPro.sh executes. It may be worth considering updating the executable to usetype -poverwhich. This is more modern/avoids clashes of differingwhichbehavior. Maybe better would be to follow a more standard installation approach like make.