Singularity Build gramtools issue

[mezewudo]

Hello: The singularity image build command fails at the point of installing gramtools below is a snapshot of the command and error messages:

singularity build clockwork_container.img clockwork_container.def

____ gramtools _____# pip3 install --process-dependency-links wheel git+https://github.com/iqbal-lab-org/gramtools@9313eceb606a6fc159e4a14c168b7a6f888c5ed2

• pip3 install --process-dependency-links wheel git+https://github.com/iqbal-lab-org/gramtools@9313eceb606a6fc159e4a14c168b7a6f888c5ed2 Collecting git+https://github.com/iqbal-lab-org/gramtools@9313eceb606a6fc159e4a14c168b7a6f888c5ed2 Cloning https://github.com/iqbal-lab-org/gramtools (to 9313eceb606a6fc159e4a14c168b7a6f888c5ed2) to /tmp/pip-041uygn9-build Could not find a tag or branch '9313eceb606a6fc159e4a14c168b7a6f888c5ed2', assuming commit. DEPRECATION: Dependency Links processing has been deprecated and will be removed in a future release. Requirement already satisfied: wheel in /usr/lib/python3/dist-packages Collecting cluster_vcf_records>=0.9.2 (from gramtools==1.6.0) Downloading https://files.pythonhosted.org/packages/74/36/4285d072b4ac0d16ec278b1fe386ced0313cd8888fa90d26d2562b58f049/cluster_vcf_records-0.13.2.tar.gz Collecting py-cortex-api>=1.0 (from gramtools==1.6.0) Downloading https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz Requirement already satisfied: pyvcf>=0.6.8 in /usr/local/lib/python3.6/dist-packages (from gramtools==1.6.0) Requirement already satisfied: scipy>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from gramtools==1.6.0) Collecting bitarray (from cluster_vcf_records>=0.9.2->gramtools==1.6.0) Downloading https://files.pythonhosted.org/packages/57/3d/db2c679f5343f7bb79ccd7366441d9e872f60c8e499e15b95551dce9a5ea/bitarray-2.0.0.tar.gz (70kB) 100% |################################| 71kB 6.5MB/s

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SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/tmp/pip-041uygn9-build/cmake-build-release/libgramtools/include'. The library files are located in '/tmp/pip-041uygn9-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-041uygn9-build/cmake-build-release/libgramtools/include -L/tmp/pip-041uygn9-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-041uygn9-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-o6jmmrip-record/install-record.txt --single-version-externally-managed --compile" failed with error code 255 in /tmp/pip-041uygn9-build/ FATAL: While performing build: while running engine: exit status 1