Install MATLAB Compiler Runtime on project Docker container

[jaclyn-taroni]

Purpose/implementation Section

I am opening this draft pull request to take advantage of the Docker layer cache in Circle to test Docker builds.

What GitHub issue does your pull request address?

#529

[jaclyn-taroni]

@jashapiro any ideas as to why the copy number consensus is failing: https://circleci.com/gh/AlexsLemonade/OpenPBTA-analysis/3144

[jashapiro]

RElevant: gnu-octave/symbolic#63

[jashapiro]

This is always a fun kind of comment:

Making the library coming with matlab invisible/unloadable solved the
problem, but maybe i will encounter some side effects ...
gnu-octave/symbolic#905 (comment)

[jaclyn-taroni]

@cgreene - I expect this to fail on the last step with something like:

Setting Matlab MCR root to /rocker-build/gistic_install/MATLAB_Compiler_Runtime
./gp_gistic2_from_seg: error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory

Except it will also complain about version -- we can set the version in the gistic2 executable that's included in the root directory of the GISTIC download. But notably ☝️ is the error I got when installing 2014a which matches the version in the GISTIC instructions.

[jaclyn-taroni]

Additional context -- contents of gistic2 are:

#!/bin/sh
## set MCR environment and launch GISTIC executable

## NOTE: change the line below if you have installed the Matlab MCR in an alternative location
MCR_ROOT=`pwd`/MATLAB_Compiler_Runtime
MCR_VER=v83

echo Setting Matlab MCR root to $MCR_ROOT

## set up environment variables
LD_LIBRARY_PATH=$MCR_ROOT/$MCR_VER/runtime/glnxa64:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=$MCR_ROOT/$MCR_VER/bin/glnxa64:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=$MCR_ROOT/$MCR_VER/sys/os/glnxa64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
XAPPLRESDIR=$MCR_ROOT/$MCR_VER/MATLAB_Component_Runtime/v83/X11/app-defaults
export XAPPLRESDIR

## launch GISTIC executable
./gp_gistic2_from_seg $@

[jaclyn-taroni]

FWIW, I got the same error building locally that shows up in CI right now.

[jaclyn-taroni]

@cgreene I think the move ™️ is going to be dealing with the MCR environmental variables at the time that we run GISTIC

[cgreene]

Looks good to me!