Install for minos is broken gramtools dependency issue

[annacprice]

Install for minos fails due to broken install of gramtools@9313eceb606a6fc159e4a14c168b7a6f888c5ed2

E.g. when building from the Singularity.def in this repo

SUCCESS: sdsl was installed successfully!
    The sdsl include files are located in '/tmp/pip-of5i099r-build/cmake-build-release/libgramtools/include'.
    The library files are located in '/tmp/pip-of5i099r-build/cmake-build-release/libgramtools/lib'.

    Sample programs can be found in the examples-directory.
    A program 'example.cpp' can be compiled with the command:
    g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
       -I/tmp/pip-of5i099r-build/cmake-build-release/libgramtools/include -L/tmp/pip-of5i099r-build/cmake-build-release/libgramtools/lib \
       example.cpp -lsdsl -ldivsufsort -ldivsufsort64

    Tests in the test-directory
    A cheat sheet in the extras/cheatsheet-directory.
    Have fun!
    [ 28%] No install step for 'sdsl'
    [ 29%] No test step for 'sdsl'
    [ 30%] Completed 'sdsl'
    [ 30%] Built target sdsl
    Makefile:83: recipe for target 'all' failed
    make: *** [all] Error 2
    ERROR: gramtools backend compilation returned:  2

    ----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-of5i099r-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-7vv5y6wr-record/install-record.txt --single-version-externally-managed --compile" failed with error code 255 in /tmp/pip-of5i099r-build/
FATAL:   failed to execute %post proc: exit status 1
FATAL:   While performing build: while running engine: while running /usr/local/libexec/singularity/bin/starter: exit status 255

This issue also causes the clockwork container build to fail. See issue [86]

Gramtools v1.8.0 installs correctly. Potentially minos needs to be updated to work with gramtools v1.8.0

[martinghunt]

Thanks for reporting, and for linking to clockwork issue. Will fix that next ...

Is now fixed on master branch of minos. We're sticking with an old commit of gramtools because minos has been heavily tested against it.

[martinghunt]

... for the record, minos commit is https://github.com/iqbal-lab-org/minos/commit/35e529b2621edbec3bb6a9fc1508f7a219615724