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{bio}[foss/2018b] pangolin 3.0.5 w/ Python 3.7.0 and dependencies #13119

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{bio}[foss/2018b] pangolin 3.0.5 w/ Python 3.7.0 and dependencies #13119

wants to merge 4 commits into from

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SethosII
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@SethosII SethosII commented Jun 11, 2021 •
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(created using eb --new-pr)

This is my attempt to build pangolin from source.

They don't give instructions to build it from source and suggest to resort to conda: https://cov-lineages.org/pangolin_docs/installation.html. I based my attempt on their environment.yml. Some dependencies are given with fixed and/or more recent versions, than what is currently used in the foss-2018b toolchain therefore the checks are failing.

This replaces #13069.

@SethosII
adding easyconfigs: Biopython-1.74-foss-2018b-Python-3.7.0.eb, Boost-…
0f4a230 
…1.68.0-foss-2018b-Python-3.7.0.eb, Bottleneck-1.3.2-foss-2018b-Python-3.7.0.eb, GitPython-2.1.11-foss-2018b-Python-3.7.0.eb, numexpr-2.6.5-foss-2018b-Python-3.7.0.eb, pandas-1.0.1-foss-2018b-Python-3.7.0.eb, pangolin-3.0.5-foss-2018b-Python-3.7.0.eb, protobuf-python-3.12.4-foss-2018b-Python-3.7.0.eb, Pysam-0.16.0.1-foss-2018b-Python-3.7.0.eb, PyYAML-3.13-foss-2018b-Python-3.7.0.eb, snakemake-5.13.0-foss-2018b-Python-3.7.0.eb, UShER-0.3.1-foss-2018b-Python-3.7.0.eb
@SethosII SethosII changed the title {bio}[foss/2018b] Biopython v1.74, Boost v1.68.0, Bottleneck v1.3.2, ... w/ Python 3.7.0 {bio}[foss/2018b] pangolin 3.0.5 w/ Python 3.7.0 and dependencies Jun 11, 2021
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@SethosII: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/928501881
Output from first failing test suite run:

('/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb', [])
ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
('/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb', [])
Check whether any conflicts occur in software dependency graphs.
('/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb', [])
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 156, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: tbb/2019_U9-foss-2018b, gofasta/0.0.4, protobuf/3.12.4-foss-2018b, minimap2/2.17-foss-2018b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 140, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: tbb/2019_U9-foss-2018b, gofasta/0.0.4, protobuf/3.12.4-foss-2018b, minimap2/2.17-foss-2018b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 541, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: tbb/2019_U9-foss-2018b, gofasta/0.0.4, protobuf/3.12.4-foss-2018b, minimap2/2.17-foss-2018b (no easyconfig file or existing module found)'

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 991, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 803, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'PythonBundle' easyblock should be used for bundle of Python packages in GitPython-2.1.11-foss-2018b-Python-3.7.0.eb
'download_dep_fail' should be set in PyYAML-3.13-foss-2018b-Python-3.7.0.eb
'source_urls' should not be defined when using the default value in PyYAML-3.13-foss-2018b-Python-3.7.0.eb
'use_pip' should be set in PyYAML-3.13-foss-2018b-Python-3.7.0.eb
sanity_pip_check should be enabled in PyYAML-3.13-foss-2018b-Python-3.7.0.eb

----------------------------------------------------------------------
Ran 12393 tests in 466.450s

FAILED (failures=1, errors=3)
ERROR: Not all tests were successful.

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Please talk to my owner @boegel if you notice you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

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@SethosII: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/928598086
Output from first failing test suite run:

======================================================================
	Bottleneck-1.3.2-foss-2018b-Python-3.7.0.eb
	GitPython-2.1.11-foss-2018b-Python-3.7.0.eb
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
	gofasta-0.0.4.eb
----------------------------------------------------------------------
	minimap2-2.17-foss-2018b.eb
Traceback (most recent call last):
	numexpr-2.6.5-foss-2018b-Python-3.7.0.eb
  File "test/easyconfigs/easyconfigs.py", line 607, in test_dep_versions_per_toolchain_generation
	PyYAML-3.13-foss-2018b-Python-3.7.0.eb
    self.assertFalse(multi_dep_vars, error_msg)
	Pysam-0.16.0.1-foss-2018b-Python-3.7.0.eb
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>201[89][ab]).*\.eb$' easyconfigs:
	pandas-1.0.1-foss-2018b-Python-3.7.0.eb

	pangolin-3.0.5-foss-2018b-Python-3.7.0.eb
found 3 variants of 'Biopython' dependency in easyconfigs using '2018b' toolchain generation
	protobuf-python-3.12.4-foss-2018b-Python-3.7.0.eb
* version: 1.72; versionsuffix: -Python-2.7.15 as dep for set(['seq2HLA-2.3-foss-2018b-Python-2.7.15.eb', 'rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb', 'MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb', 'Seqmagick-0.6.2-foss-2018b-Python-2.7.15.eb', 'nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb', 'metaWRAP-1.2-foss-2018b-Python-2.7.15.eb', 'nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb', 'VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb', 'CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb', 'FlexiDot-1.06-foss-2018b-Python-2.7.15.eb'])
	protobuf-3.12.4-foss-2018b.eb
* version: 1.72; versionsuffix: -Python-3.6.6 as dep for set(['smallgenomeutilities-0.2.1-foss-2018b-Python-3.6.6.eb', 'MitoZ-2.3-foss-2018b-Python-3.6.6.eb', 'nanofilt-2.5.0-foss-2018b-Python-3.6.6.eb', 'medaka-0.12.0-foss-2018b-Python-3.6.6.eb', 'artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb', 'medaka-0.11.4-foss-2018b-Python-3.6.6.eb', 'rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb', 'medaka-0.4.3-foss-2018b-Python-3.6.6.eb', 'nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb', 'amplimap-0.4.16-foss-2018b-Python-3.6.6.eb'])
	snakemake-5.13.0-foss-2018b-Python-3.7.0.eb
* version: 1.74; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb'])
	tbb-2019_U9-foss-2018b.eb

	UShER-0.3.1-foss-2018b-Python-3.7.0.eb
found 2 variants of 'Boost' dependency in easyconfigs using '2018b' toolchain generation
* version: 1.67.0; versionsuffix:  as dep for set(['MITObim-1.9.1-foss-2018b.eb', 'crb-blast-0.6.9-foss-2018b-Ruby-2.6.1.eb', 'Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb', 'Spark-2.4.0-foss-2018b-Python-2.7.15.eb', 'lrslib-6.2-intel-2018b.eb', 'BLAST+-2.8.1-foss-2018b.eb', 'rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb', 'THetA-0.7-foss-2018b-Python-2.7.15.eb', 'Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb', 'Spark-3.0.0-intel-2018b-Python-2.7.15.eb', 'Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb', 'Boost.Python-1.67.0-intel-2018b-Python-3.6.6.eb', 'VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb', 'MIRA-4.0.2-foss-2018b.eb', 'Normaliz-3.6.3-intel-2018b.eb', 'POV-Ray-3.7.0.7-foss-2018b.eb', 'Spark-3.0.0-foss-2018b-Python-2.7.15.eb', 'bmtagger-3.101-foss-2018b.eb', 'OpenFOAM-v1606+-foss-2018b.eb', 'Mothur-1.41.0-foss-2018b-Python-2.7.15.eb', 'OpenImageIO-1.8.16-foss-2018b.eb', 'shovill-1.0.4-foss-2018b-Python-2.7.15.eb', 'OpenFOAM-v1812-foss-2018b.eb', 'gap-4.9.3-intel-2018b.eb', 'QDD-3.1.2-intel-2018b-Perl-5.28.0.eb', 'OpenImageIO-1.8.16-intel-2018b.eb', 'scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb', 'MitoZ-2.3-foss-2018b-Python-3.6.6.eb', 'strelka-2.9.10-intel-2018b-Python-2.7.15.eb', 'Armadillo-9.600.5-foss-2018b.eb', 'MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb', 'SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb', 'Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb', 'Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb', 'OpenFOAM-6-foss-2018b.eb', 'strelka-2.9.10-foss-2018b-Python-2.7.15.eb', 'MariaDB-10.3.10-foss-2018b.eb', 'Arrow-0.12.0-intel-2018b-Python-3.6.6.eb', 'MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb', 'metaWRAP-1.2-foss-2018b-Python-2.7.15.eb', 'PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb', 'OpenFOAM-v1612+-foss-2018b.eb', 'DBD-mysql-4.048-foss-2018b-Perl-5.28.0.eb', 'Boost.Python-1.67.0-intel-2018b-Python-2.7.15.eb', 'strelka-2.9.9-foss-2018b.eb', 'AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb', 'TopHat-2.1.2-foss-2018b.eb', 'libosmium-2.15.4-foss-2018b-Python-3.6.6.eb', 'ArrayFire-3.6.4-foss-2018b.eb', 'SKESA-2.3.0-foss-2018b.eb', 'TiMBL-6.4.13-intel-2018b.eb', 'CGAL-4.11.1-foss-2018b-Python-3.6.6.eb', 'OpenFOAM-v1806-foss-2018b.eb', 'DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb', 'Cufflinks-2.2.1-foss-2018b.eb', 'MaSuRCA-3.3.1-foss-2018b-Perl-5.28.0.eb', 'FastQTL-2.184-foss-2018b.eb', 'QUAST-5.0.2-foss-2018b-Python-2.7.15.eb', 'IntaRNA-2.3.1-foss-2018b-Python-2.7.15.eb', 'Boost.Python-1.67.0-fosscuda-2018b-Python-2.7.15.eb', 'Arrow-0.12.0-intel-2018b-Python-2.7.15.eb', 'ChimPipe-0.9.5-foss-2018b.eb', 'Salmon-0.12.0-foss-2018b.eb', 'OrthoFinder-2.3.3-intel-2018b-Python-2.7.15.eb', 'VEP-94.0-foss-2018b-Perl-5.28.0.eb', 'bnpy-0.1.6-foss-2018b-Python-2.7.15.eb', 'taxator-tk-1.3.3-foss-2018b.eb', 'canu-1.8-foss-2018b-Perl-5.28.0.eb', 'SCIPhI-0.1.3-intel-2018b.eb', 'CGAL-4.11.1-foss-2018b-Python-2.7.15.eb', 'BLAST+-2.7.1-foss-2018b.eb', 'Arrow-0.12.0-foss-2018b-Python-2.7.15.eb', 'Amber-18-fosscuda-2018b-AmberTools-18-patchlevel-10-8.eb', 'graph-tool-2.27-foss-2018b-Python-3.6.6.eb', 'Salmon-0.14.1-foss-2018b.eb', 'TiCCutils-0.21-intel-2018b.eb', 'RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb', 'BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb', 'Boost.Python-1.67.0-foss-2018b-Python-2.7.15.eb', 'VEP-95.0-foss-2018b-Perl-5.28.0.eb', 'ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb', 'Blender-2.79b-intel-2018b-Python-3.6.6.eb', 'Spark-2.4.0-intel-2018b-Python-2.7.15.eb', 'OpenMS-2.4.0-foss-2018b.eb', 'Spark-2.4.0-intel-2018b-Python-3.6.6.eb', 'POV-Ray-3.7.0.7-intel-2018b.eb', 'BLAST+-2.7.1-intel-2018b.eb'])
* version: 1.68.0; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'UShER-0.3.1-foss-2018b-Python-3.7.0.eb'])

found 2 variants of 'GitPython' dependency in easyconfigs using '2018b' toolchain generation
* version: 2.1.11; versionsuffix: -Python-3.6.6 as dep for set(['snakemake-5.2.4-intel-2018b-Python-3.6.6.eb', 'artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb', 'snakemake-5.2.4-foss-2018b-Python-3.6.6.eb', 'rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb', 'amplimap-0.4.16-foss-2018b-Python-3.6.6.eb'])
* version: 2.1.11; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'snakemake-5.13.0-foss-2018b-Python-3.7.0.eb'])

found 3 variants of 'PyYAML' dependency in easyconfigs using '2018b' toolchain generation
* version: 3.13; versionsuffix: -Python-2.7.15 as dep for set(['Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb', 'dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb', 'phonopy-1.14.2-intel-2018b-Python-2.7.15.eb', 'MultiQC-1.7-intel-2018b-Python-2.7.15.eb'])
* version: 3.13; versionsuffix: -Python-3.6.6 as dep for set(['MultiQC-1.7-intel-2018b-Python-3.6.6.eb', 'scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb', 'bokeh-1.0.4-intel-2018b-Python-3.6.6.eb', 'snakemake-5.2.4-intel-2018b-Python-3.6.6.eb', 'imgaug-0.2.8-foss-2018b-Python-3.6.6.eb', 'awscli-1.16.290-foss-2018b-Python-3.6.6.eb', 'dask-1.0.0-intel-2018b-Python-3.6.6.eb', 'dask-0.19.4-intel-2018b-Python-3.6.6.eb', 'dask-0.19.4-foss-2018b-Python-3.6.6.eb', 'scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb', 'pyqstem-1.0.3-foss-2018b-Python-3.6.6.eb', 'scikit-image-0.14.1-intel-2018b-Python-3.6.6.eb', 'PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb', 'MultiQC-1.7-foss-2018b-Python-3.6.6.eb', 'torchvision-0.2.2-foss-2018b-Python-3.6.6.eb', 'medaka-0.4.3-foss-2018b-Python-3.6.6.eb', 'pyqstem-1.0.3-intel-2018b-Python-3.6.6.eb', 'bokeh-1.0.4-foss-2018b-Python-3.6.6.eb', 'FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb', 'amplimap-0.4.16-foss-2018b-Python-3.6.6.eb', 'Keras-2.2.4-fosscuda-2018b-Python-3.6.6.eb', 'dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb', 'torchvision-0.2.2-fosscuda-2018b-Python-3.6.6.eb', 'PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb', 'bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb', 'snakemake-5.2.4-foss-2018b-Python-3.6.6.eb', 'Keras-2.2.4-foss-2018b-Python-3.6.6.eb', 'scikit-image-0.14.1-foss-2018b-Python-3.6.6.eb', 'scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb', 'dask-1.0.0-foss-2018b-Python-3.6.6.eb', 'rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb', 'artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb', 'limix-2.0.4-foss-2018b-Python-3.6.6.eb'])
* version: 3.13; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'snakemake-5.13.0-foss-2018b-Python-3.7.0.eb'])

found 3 variants of 'Pysam' dependency in easyconfigs using '2018b' toolchain generation
* version: 0.15.1; versionsuffix: -Python-2.7.15 as dep for set(['CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb', 'SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb', 'OptiType-1.3.2-foss-2018b-Python-2.7.15.eb', 'nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb', 'metaWRAP-1.2-foss-2018b-Python-2.7.15.eb', 'nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb', 'HTSeq-0.11.0-foss-2018b-Python-2.7.15.eb', 'CheckM-1.0.13-foss-2018b-Python-2.7.15.eb', 'stpipeline-1.7.3-foss-2018b-Python-2.7.15.eb', 'HTSeq-0.11.0-intel-2018b-Python-2.7.15.eb'])
* version: 0.15.1; versionsuffix: -Python-3.6.6 as dep for set(['RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb', 'smallgenomeutilities-0.2.1-foss-2018b-Python-3.6.6.eb', 'pybedtools-0.7.10-foss-2018b-Python-3.6.6.eb', 'VAtools-3.0.1-foss-2018b-Python-3.6.6.eb', 'CITE-seq-Count-1.4.3-foss-2018b-Python-3.6.6.eb', 'medaka-0.11.4-foss-2018b-Python-3.6.6.eb', 'split-seq-20190717-foss-2018b-Python-3.6.6.eb', 'iCount-20180820-foss-2018b-Python-3.6.6.eb', 'UMI-tools-1.0.0-foss-2018b-Python-3.6.6.eb', 'deepTools-3.3.1-foss-2018b-Python-3.6.6.eb', 'medaka-0.4.3-foss-2018b-Python-3.6.6.eb', 'nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb', 'medaka-0.12.0-foss-2018b-Python-3.6.6.eb', 'RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb', 'HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb', 'OptiType-1.3.2-foss-2018b-Python-3.6.6.eb', 'RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb', 'artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb'])
* version: 0.16.0.1; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb'])

found 3 variants of 'Python' dependency in easyconfigs using '2018b' toolchain generation
* version: 2.7.15; versionsuffix:  as dep for set(['FSL-5.0.11-foss-2018b.eb', 'PHLAT-1.1-foss-2018b-Python-2.7.15.eb', 'ViennaRNA-2.4.10-foss-2018b-Python-2.7.15.eb', 'CESM-deps-2-intel-2018b.eb', 'Assimulo-2.9-intel-2018b-Python-2.7.15.eb', 'gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb', 'Spark-2.4.0-foss-2018b-Python-2.7.15.eb', 'cftime-1.0.1-intel-2018b-Python-2.7.15.eb', 'CESM-deps-2-iomkl-2018b.eb', 'PyFMI-2.4.0-intel-2018b-Python-2.7.15.eb', 'Vim-8.1.0483-foss-2018b-Python-2.7.15.eb', 'Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb', 'GRASS-7.6.0-foss-2018b-Python-2.7.15.eb', 'Pysam-0.15.1-foss-2018b-Python-2.7.15.eb', 'Sphinx-1.8.1-foss-2018b-Python-2.7.15.eb', 'THetA-0.7-foss-2018b-Python-2.7.15.eb', 'PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb', 'Spark-3.0.0-intel-2018b-Python-2.7.15.eb', 'Mako-1.0.7-foss-2018b-Python-2.7.15.eb', 'GConf-3.2.6-foss-2018b.eb', 'psutil-5.4.7-foss-2018b-Python-2.7.15.eb', 'scp-0.13.1-intel-2018b-Python-2.7.15.eb', 'VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb', 'Spark-3.0.0-foss-2018b-Python-2.7.15.eb', 'GDAL-2.2.3-foss-2018b-Python-2.7.15.eb', 'DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb', 'OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb', 'VTK-8.1.1-foss-2018b-Python-2.7.15.eb', 'Tkinter-2.7.15-fosscuda-2018b-Python-2.7.15.eb', 'pytest-4.4.0-foss-2018b-Python-2.7.15.eb', 'h5py-2.8.0-intel-2018b-Python-2.7.15-serial.eb', 'networkx-2.2-intel-2018b-Python-2.7.15.eb', 'lxml-4.2.5-intel-2018b-Python-2.7.15.eb', 'Pillow-5.3.0-foss-2018b-Python-2.7.15.eb', 'bitarray-0.8.3-intel-2018b-Python-2.7.15.eb', 'Mako-1.0.7-intel-2018b-Python-2.7.15.eb', 'IPython-5.8.0-intel-2018b-Python-2.7.15.eb', 'pkgconfig-1.3.1-intel-2018b-Python-2.7.15.eb', 'CompareM-0.0.23-foss-2018b-Python-2.7.15.eb', 'cutadapt-1.18-foss-2018b-Python-2.7.15.eb', 'PyCogent-1.9-foss-2018b-Python-2.7.15.eb', 'OpenFOAM-v1606+-foss-2018b.eb', 'sep-1.0.3-foss-2018b-Python-2.7.15.eb', 'Pysam-0.15.1-intel-2018b-Python-2.7.15.eb', 'Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb', 'pyfits-3.5-intel-2018b-Python-2.7.15.eb', 'ITK-4.13.1-foss-2018b-Python-2.7.15.eb', 'PyYAML-3.13-intel-2018b-Python-2.7.15.eb', 'numexpr-2.6.5-foss-2018b-Python-2.7.15.eb', 'Boost-1.68.0-foss-2018b-Python-2.7.15.eb', 'Theano-1.0.2-fosscuda-2018b-Python-2.7.15.eb', 'shovill-1.0.4-foss-2018b-Python-2.7.15.eb', 'wxPython-3.0.2.0-foss-2018b-Python-2.7.15.eb', 'Pylint-1.9.3-intel-2018b-Python-2.7.15.eb', 'Biopython-1.72-foss-2018b-Python-2.7.15.eb', 'Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb', 'scp-0.13.2-intel-2018b-Python-2.7.15.eb', 'p4vasp-0.3.30-foss-2018b-Python-2.7.15.eb', 'MEGAHIT-1.1.4-foss-2018b-Python-2.7.15.eb', 'PyCairo-1.18.0-foss-2018b-Python-2.7.15.eb', 'libgpuarray-0.7.6-fosscuda-2018b-Python-2.7.15.eb', 'ROOT-6.14.06-foss-2018b-Python-2.7.15.eb', 'matplotlib-2.2.3-fosscuda-2018b-Python-2.7.15.eb', 'netcdf4-python-1.4.1-intel-2018b-Python-2.7.15.eb', 'GST-plugins-base-0.10.36-foss-2018b.eb', 'emcee-2.2.1-foss-2018b-Python-2.7.15.eb', 'PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb', 'plc-3.0.1-intel-2018b-Python-2.7.15.eb', 'tqdm-4.24.0-foss-2018b-Python-2.7.15.eb', 'GATE-8.2-foss-2018b-Python-2.7.15.eb', 'scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb', 'Inelastica-1.3.5-intel-2018b-Python-2.7.15.eb', 'TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb', 'Flye-2.4-intel-2018b-Python-2.7.15.eb', 'h5py-2.8.0-foss-2018b-Python-2.7.15.eb', 'GEOS-3.6.2-foss-2018b-Python-2.7.15.eb', 'dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb', 'dtcwt-0.12.0-foss-2018b-Python-2.7.15.eb', 'Mothur-1.41.0-foss-2018b-Python-2.7.15.eb', 'strelka-2.9.10-intel-2018b-Python-2.7.15.eb', 'GObject-Introspection-1.54.1-foss-2018b-Python-2.7.15.eb', 'TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb', 'IPython-5.8.0-foss-2018b-Python-2.7.15.eb', 'MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb', 'sympy-1.3-foss-2018b-Python-2.7.15.eb', 'OpenFOAM-v1812-foss-2018b.eb', 'CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb', 'stpipeline-1.7.3-foss-2018b-Python-2.7.15.eb', 'HTSeq-0.11.0-intel-2018b-Python-2.7.15.eb', 'PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb', 'Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb', 'molmod-1.4.4-intel-2018b-Python-2.7.15.eb', 'MinPath-1.4-intel-2018b-Python-2.7.15.eb', 'Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb', 'SWIG-3.0.12-intel-2018b-Python-2.7.15.eb', 'SCons-3.0.4-foss-2018b-Python-2.7.15.eb', 'BlobTools-20180528-foss-2018b-Python-2.7.15.eb', 'OpenFOAM-6-foss-2018b.eb', 'GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb', 'Tkinter-2.7.15-intel-2018b-Python-2.7.15.eb', 'emcee-2.2.1-intel-2018b-Python-2.7.15.eb', 'Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb', 'Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb', 'Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb', 'SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb', 'MagresPython-20160329-foss-2018b-Python-2.7.15.eb', 'GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb', 'MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb', 'Seqmagick-0.6.2-foss-2018b-Python-2.7.15.eb', 'protobuf-python-3.6.0-fosscuda-2018b-Python-2.7.15.eb', 'metaWRAP-1.2-foss-2018b-Python-2.7.15.eb', 'horton-2.1.1-foss-2018b-Python-2.7.15.eb', 'matplotlib-2.2.3-foss-2018b-Python-2.7.15.eb', 'Boost.Python-1.67.0-intel-2018b-Python-2.7.15.eb', 'networkx-2.2-foss-2018b-Python-2.7.15.eb', 'Pylint-1.9.3-iomkl-2018b-Python-2.7.15.eb', 'seq2HLA-2.3-foss-2018b-Python-2.7.15.eb', 'AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb', 'h5py-2.8.0-intel-2018b-Python-2.7.15.eb', 'pkgconfig-1.3.1-foss-2018b-Python-2.7.15.eb', 'wheel-0.31.1-fosscuda-2018b-Python-2.7.15.eb', 'Biopython-1.72-intel-2018b-Python-2.7.15.eb', 'PyYAML-3.13-fosscuda-2018b-Python-2.7.15.eb', 'horton-2.1.1-intel-2018b-Python-2.7.15.eb', 'astropy-2.0.12-intel-2018b-Python-2.7.15.eb', 'Pyomo-5.5.0-foss-2018b-Python-2.7.15.eb', 'PyGObject-2.28.7-foss-2018b-Python-2.7.15.eb', 'statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb', 'OptiType-1.3.2-foss-2018b-Python-2.7.15.eb', 'R-3.5.1-foss-2018b-Python-2.7.15.eb', 'rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb', 'PSI4-1.2.1-intel-2018b-Python-2.7.15-maxam8.eb', 'GATE-8.1.p01-foss-2018b-Python-2.7.15.eb', 'yaff-1.4.5-intel-2018b-Python-2.7.15.eb', 'CheckM-1.0.13-foss-2018b-Python-2.7.15.eb', 'OpenFOAM-v1806-foss-2018b.eb', 'DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb', 'pkgconfig-1.3.1-fosscuda-2018b-Python-2.7.15.eb', 'bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb', 'pytest-3.8.2-intel-2018b-Python-2.7.15.eb', 'Glade-3.8.6-foss-2018b-Python-2.7.15.eb', 'PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb', 'PyTables-3.4.4-foss-2018b-Python-2.7.15.eb', 'ITSTool-2.0.5-foss-2018b-Python-2.7.15.eb', 'FSL-6.0.2-foss-2018b-Python-2.7.15.eb', 'QUAST-5.0.2-foss-2018b-Python-2.7.15.eb', 'IntaRNA-2.3.1-foss-2018b-Python-2.7.15.eb', 'GenomeTools-1.5.10-foss-2018b-Python-2.7.15.eb', 'future-0.16.0-foss-2018b-Python-2.7.15.eb', 'Boost.Python-1.67.0-fosscuda-2018b-Python-2.7.15.eb', 'Arrow-0.12.0-intel-2018b-Python-2.7.15.eb', 'libspatialite-4.3.0a-foss-2018b.eb', 'TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb', 'FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb', 'FlexiDot-1.06-foss-2018b-Python-2.7.15.eb', 'GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb', 'Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb', 'matplotlib-2.2.3-intel-2018b-Python-2.7.15.eb', 'yaff-1.5.0-intel-2018b-Python-2.7.15.eb', 'GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb', 'phonopy-1.14.2-intel-2018b-Python-2.7.15.eb', 'OrthoFinder-2.3.3-intel-2018b-Python-2.7.15.eb', 'lxml-4.2.5-foss-2018b-Python-2.7.15.eb', 'h5py-2.8.0-fosscuda-2018b-Python-2.7.15.eb', 'slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb', 'ParaView-5.4.1-foss-2018b-mpi.eb', 'gdc-client-1.3.0-foss-2018b-Python-2.7.15.eb', 'bnpy-0.1.6-foss-2018b-Python-2.7.15.eb', 'PyGTK-2.24.0-foss-2018b-Python-2.7.15.eb', 'SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb', 'LMfit-0.9.14-intel-2018b-Python-2.7.15.eb', 'psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb', 'IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb', 'PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb', 'SimpleITK-1.1.0-foss-2018b-Python-2.7.15.eb', 'deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb', 'CGAL-4.11.1-foss-2018b-Python-2.7.15.eb', 'numexpr-2.6.5-intel-2018b-Python-2.7.15.eb', 'Boost-1.68.0-intel-2018b-Python-2.7.15.eb', 'astropy-2.0.12-foss-2018b-Python-2.7.15.eb', 'Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb', 'GStreamer-0.10.36-foss-2018b.eb', 'CESM-deps-2-foss-2018b.eb', 'Arrow-0.12.0-foss-2018b-Python-2.7.15.eb', 'Amber-18-fosscuda-2018b-AmberTools-18-patchlevel-10-8.eb', 'VMD-1.9.3-intel-2018b-Python-2.7.15.eb', 'NEURON-7.6.5-intel-2018b-Python-2.7.15.eb', 'OpenFOAM-v1612+-foss-2018b.eb', 'Short-Pair-20170125-foss-2018b-Python-2.7.15.eb', 'scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb', 'BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb', 'sep-1.0.3-intel-2018b-Python-2.7.15.eb', 'GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb', 'ViennaRNA-2.4.10-intel-2018b-Python-2.7.15.eb', 'OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb', 'Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb', 'Boost.Python-1.67.0-foss-2018b-Python-2.7.15.eb', 'Tkinter-2.7.15-foss-2018b-Python-2.7.15.eb', 'TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb', 'Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb', 'future-0.16.0-intel-2018b-Python-2.7.15.eb', 'psrecord-1.1-intel-2018b-Python-2.7.15.eb', 'ParaView-5.5.2-foss-2018b-Python-2.7.15-mpi.eb', 'libxml2-python-2.9.8-foss-2018b-Python-2.7.15.eb', 'scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb', 'strelka-2.9.10-foss-2018b-Python-2.7.15.eb', 'HTSeq-0.11.0-foss-2018b-Python-2.7.15.eb', 'Pylint-1.9.3-foss-2018b-Python-2.7.15.eb', 'SWIG-3.0.12-foss-2018b-Python-2.7.15.eb', 'Spark-2.4.0-intel-2018b-Python-2.7.15.eb', 'MultiQC-1.7-intel-2018b-Python-2.7.15.eb', 'OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb', 'mpmath-1.0.0-foss-2018b-Python-2.7.15.eb', 'nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb', 'SCons-3.0.1-foss-2018b-Python-2.7.15.eb', 'SCons-3.0.1-fosscuda-2018b-Python-2.7.15.eb', 'SeisSol-201703-foss-2018b-Python-2.7.15.eb', 'XMDS2-2.2.3-foss-2018b-Python-2.7.15.eb', 'nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb', 'Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb', 'MapSplice-2.2.1-intel-2018b-Python-2.7.15.eb', 'pytest-4.4.0-intel-2018b-Python-2.7.15.eb', 'PSI4-1.2.1-intel-2018b-Python-2.7.15.eb', 'statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb', 'MinPath-1.4-foss-2018b-Python-2.7.15.eb'])
* version: 3.6.6; versionsuffix:  as dep for set(['pytest-4.4.0-intel-2018b-Python-3.6.6.eb', 'graph-tool-2.27-foss-2018b-Python-3.6.6.eb', 'zingeR-20180131-foss-2018b-R-3.5.1.eb', 'libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb', 'LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb', 'R-3.5.1-foss-2018b-bare.eb', 'SWIG-3.0.12-foss-2018b-Python-3.6.6.eb', 'gmsh-3.0.6-foss-2018b-Python-3.6.6.eb', 'ASE-3.18.0-foss-2018b-Python-3.6.6.eb', 'networkx-2.2-foss-2018b-Python-3.6.6.eb', 'IPython-7.2.0-foss-2018b-Python-3.6.6.eb', 'gmsh-4.2.2-foss-2018b-Python-3.6.6.eb', 'basemap-1.2.0-intel-2018b-Python-3.6.6.eb', 'Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb', 'PyTables-3.4.4-intel-2018b-Python-3.6.6.eb', 'scikit-image-0.14.1-foss-2018b-Python-3.6.6.eb', 'simpy-3.0.11-intel-2018b-Python-3.6.6.eb', 'lxml-4.2.5-foss-2018b-Python-3.6.6.eb', 'POT-0.5.1-intel-2018b-Python-3.6.6.eb', 'GDAL-2.2.3-foss-2018b-Python-3.6.6.eb', 'Flask-1.0.2-foss-2018b-Python-3.6.6.eb', 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'imgaug-0.2.8-foss-2018b-Python-3.6.6.eb', 'RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb', 'NiBabel-2.5.1-foss-2018b-Python-3.6.6.eb', 'GitPython-2.1.11-foss-2018b-Python-3.6.6.eb', 'ETE-3.1.1-foss-2018b-Python-3.6.6.eb', 'Tkinter-3.6.6-foss-2018b-Python-3.6.6.eb', 'python-parasail-1.1.16-foss-2018b-Python-3.6.6.eb', 'DSA-1.0-foss-2018b-R-3.5.1.eb', 'Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb', 'Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb', 'Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb', 'artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb', 'pkgconfig-1.3.1-intel-2018b-Python-3.6.6.eb', 'bitarray-0.8.3-intel-2018b-Python-3.6.6.eb', 'ASE-3.17.0-intel-2018b-Python-3.6.6.eb', 'GEOS-3.6.2-intel-2018b-Python-3.6.6.eb', 'YAPS-1.1.0-foss-2018b-R-3.5.1.eb', 'cutadapt-2.1-foss-2018b-Python-3.6.6.eb', 'ASE-3.19.0-intel-2018b-Python-3.6.6.eb', 'PyQtGraph-0.10.0-intel-2018b-Python-3.6.6.eb', 'medaka-0.12.0-foss-2018b-Python-3.6.6.eb', 'protobuf-python-3.6.0-foss-2018b-Python-3.6.6.eb', 'cytoolz-0.10.1-foss-2018b-Python-3.6.6.eb', 'sympy-1.3-foss-2018b-Python-3.6.6.eb', 'Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb', 'BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb', 'VarDict-1.5.7-foss-2018b-Perl-5.28.0.eb', 'Pysolar-0.8-intel-2018b-Python-3.6.6.eb', 'rootpy-1.0.1-foss-2018b-Python-3.6.6.eb', 'scikit-build-0.10.0-intel-2018b-Python-3.6.6.eb', 'scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb', 'root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb', 'statsmodels-0.9.0-intel-2018b-Python-3.6.6.eb', 'limix-2.0.4-foss-2018b-Python-3.6.6.eb', 'Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb', 'dask-1.0.0-foss-2018b-Python-3.6.6.eb', 'MuSiC-1.6.2-foss-2018b-R-3.5.1.eb', 'Spark-2.4.0-intel-2018b-Python-3.6.6.eb', 'h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb', 'MEGAHIT-1.1.4-foss-2018b-Python-3.6.6.eb', 'sciClone-1.1-foss-2018b-R-3.5.1.eb', 'imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb', 'Keras-2.2.4-foss-2018b-Python-3.6.6.eb', 'scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb', 'RStan-2.18.2-foss-2018b-R-3.5.1.eb', 'nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb', 'netcdf4-python-1.4.3-foss-2018b-Python-3.6.6.eb', 'Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb', 'rjags-4-8-foss-2018b-R-3.5.1.eb', 'Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb', 'Pillow-SIMD-5.3.0.post0-foss-2018b-Python-3.6.6.eb', 'deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb'])
* version: 3.7.0; versionsuffix:  as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'snakemake-5.13.0-foss-2018b-Python-3.7.0.eb', 'Boost-1.68.0-foss-2018b-Python-3.7.0.eb', 'Pysam-0.16.0.1-foss-2018b-Python-3.7.0.eb', 'numexpr-2.6.5-foss-2018b-Python-3.7.0.eb', 'PyYAML-3.13-foss-2018b-Python-3.7.0.eb', 'protobuf-python-3.12.4-foss-2018b-Python-3.7.0.eb', 'pandas-1.0.1-foss-2018b-Python-3.7.0.eb', 'Biopython-1.74-foss-2018b-Python-3.7.0.eb', 'Bottleneck-1.3.2-foss-2018b-Python-3.7.0.eb', 'GitPython-2.1.11-foss-2018b-Python-3.7.0.eb', 'UShER-0.3.1-foss-2018b-Python-3.7.0.eb'])

found 2 variants of 'minimap2' dependency in easyconfigs using '2018b' toolchain generation
* version: 2.13; versionsuffix:  as dep for set(['SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb', 'medaka-0.12.0-foss-2018b-Python-3.6.6.eb', 'artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb', 'medaka-0.11.4-foss-2018b-Python-3.6.6.eb', 'rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb', 'medaka-0.4.3-foss-2018b-Python-3.6.6.eb', 'nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb'])
* version: 2.17; versionsuffix:  as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb'])

found 3 variants of 'numexpr' dependency in easyconfigs using '2018b' toolchain generation
* version: 2.6.5; versionsuffix: -Python-2.7.15 as dep for set(['bnpy-0.1.6-foss-2018b-Python-2.7.15.eb', 'PyTables-3.4.4-foss-2018b-Python-2.7.15.eb', 'OptiType-1.3.2-foss-2018b-Python-2.7.15.eb', 'THetA-0.7-foss-2018b-Python-2.7.15.eb'])
* version: 2.6.5; versionsuffix: -Python-3.6.6 as dep for set(['PyTables-3.4.4-fosscuda-2018b-Python-3.6.6.eb', 'PyTables-3.4.4-foss-2018b-Python-3.6.6.eb', 'OptiType-1.3.2-foss-2018b-Python-3.6.6.eb', 'PyTables-3.4.4-intel-2018b-Python-3.6.6.eb', 'rootpy-1.0.1-foss-2018b-Python-3.6.6.eb'])
* version: 2.6.5; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'pandas-1.0.1-foss-2018b-Python-3.7.0.eb'])

found 2 variants of 'protobuf' dependency in easyconfigs using '2018b' toolchain generation
* version: 3.12.4; versionsuffix:  as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'protobuf-python-3.12.4-foss-2018b-Python-3.7.0.eb', 'UShER-0.3.1-foss-2018b-Python-3.7.0.eb'])
* version: 3.6.0; versionsuffix:  as dep for set(['protobuf-python-3.6.0-foss-2018b-Python-3.6.6.eb', 'TensorFlow-1.11.0-foss-2018b-Python-3.6.6.eb', 'Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb', 'DeepSurv-2.0.0-20180922-fosscuda-2018b-Python-3.6.6.eb', 'TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb', 'protobuf-python-3.6.0-fosscuda-2018b-Python-2.7.15.eb', 'TensorFlow-1.10.1-foss-2018b-Python-3.6.6.eb', 'protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb', 'TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb'])

found 3 variants of 'protobuf-python' dependency in easyconfigs using '2018b' toolchain generation
* version: 3.12.4; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'UShER-0.3.1-foss-2018b-Python-3.7.0.eb'])
* version: 3.6.0; versionsuffix: -Python-2.7.15 as dep for set(['TensorFlow-1.10.0-fosscuda-2018b-Python-2.7.15.eb', 'Keras-2.2.2-fosscuda-2018b-Python-2.7.15.eb', 'TensorFlow-1.10.1-fosscuda-2018b-Python-2.7.15.eb'])
* version: 3.6.0; versionsuffix: -Python-3.6.6 as dep for set(['TensorFlow-1.10.1-foss-2018b-Python-3.6.6.eb', 'TensorFlow-1.11.0-foss-2018b-Python-3.6.6.eb', 'DeepSurv-2.0.0-20180922-fosscuda-2018b-Python-3.6.6.eb'])

found 2 variants of 'snakemake' dependency in easyconfigs using '2018b' toolchain generation
* version: 5.13.0; versionsuffix: -Python-3.7.0 as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb'])
* version: 5.2.4; versionsuffix: -Python-3.6.6 as dep for set(['artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb', 'rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb', 'amplimap-0.4.16-foss-2018b-Python-3.6.6.eb'])

found 2 variants of 'tbb' dependency in easyconfigs using '2018b' toolchain generation
* version: 2018_U5; versionsuffix:  as dep for set(['CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb', 'SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb', 'Bowtie2-2.3.4.2-foss-2018b.eb', 'miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb', 'PHLAT-1.1-foss-2018b-Python-2.7.15.eb', 'Bowtie-1.2.3-foss-2018b.eb', 'Flexbar-3.5.0-foss-2018b.eb', 'FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb', 'Bowtie2-2.3.4.2-intel-2018b.eb', 'Salmon-0.14.1-foss-2018b.eb', 'Trinity-2.8.4-foss-2018b.eb', 'Bismark-0.20.1-foss-2018b.eb', 'MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb', 'MetaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb', 'Bismark-0.20.1-intel-2018b.eb', 'metaWRAP-1.2-foss-2018b-Python-2.7.15.eb', 'Bowtie-1.2.2-foss-2018b.eb', 'Salmon-0.12.0-foss-2018b.eb'])
* version: 2019_U9; versionsuffix:  as dep for set(['pangolin-3.0.5-foss-2018b-Python-3.7.0.eb', 'UShER-0.3.1-foss-2018b-Python-3.7.0.eb'])


----------------------------------------------------------------------
Ran 12397 tests in 401.558s

FAILED (failures=1)
ERROR: Not all tests were successful.

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

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Test report by @SethosII
SUCCESS
Build succeeded for 17 out of 17 (16 easyconfigs in total)
ribnode015 - Linux ubuntu 18.04, x86_64, Intel(R) Xeon(R) CPU E5645 @ 2.40GHz, Python 2.7.17
See https://gist.github.com/e37b65d9aea2343d72e8062c6fe5b17a for a full test report.

@sassy-crick
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@SethosII I am working on Pangolin-3.1.9. Want to join force? Are you on the EasyBuild Slack?

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SethosII commented Aug 7, 2021

@sassy-crick Of course, you're welcome! But I'm not on Slack.

I also have an easyconfig for pangolin/3.1.5 with foss/2018b, so it should be only a matter of changing the version numbers and checksums. I haven't created a pull request for it because nobody seemed to be interested in pangolin until now :)

What toolchain are you using? I will also create one for foss/2021a (or gompi/2021a/GCC-10.3.0 respectively).

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@SethosII Sounds good to me. I was aiming for the foss-2021a or so as well, i.e. the latest one. I was working on usher-0.4.1 which requires TBB as you know and here I hit this wall on Friday. This is when I called it a day as it was late.
I got Snakemake and minimap2 merged and gofasta as PR open. I also have Biopython-1.79 for foss-2021a if that helps but not as a PR (see PR 13574 for discussion).
I might use an earlier version of TBB to get that moving which is not something I would like to do as I prefer to have the latest software if possible when I do EC.
I have not done yet: pangoLEARN, scorpio, constellations, pango-designation
Hope that helps.

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@sassy-crick Sorry for the delay. Yes, TBB is also needed for other stuff and I'm stuck there as well. I would also prefer the most recent version. A Biopython-1.79-foss-2021a.eb EasyConfig already exists. I include pangoLEARN, scorpio, constellations and pango-designation as extensions in my pangolin EasyConfigs. I will create a new PR for 2021a and link it here.

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@SethosII That would be great if you can do that! I think we now have all the relavants bits in place apart from the user
If you like, I can finish off my EC I started when I hit the TBB problem. Do you happen to know if TBB is used in any of the other programs we need for pangolin ? I have not seen it but it is better to double check. So, I would suggest given the current stopper to use a slightly older version of TBB which does not show that problem so we can move forward.
All of the programs I mentioned above are merged as far as I can see.
So if you are happy, I can do the usher and you can finish off the pangolin ?
I think we are getting there. 👍

@SethosII SethosII mentioned this pull request Aug 10, 2021
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@sassy-crick I created the PR for pangolin: #13681.

There is no other dependency in pangolin that needs TBB. I would recommend to create an EasyConfig for usher with the current tbb version and hope that the PR for tbb gets resolved. Maybe we can give a reminder in the tbb PR on the importance for other software.

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@sassy-crick Many thanks! I have downloaded the PR and I am updating it to the latest toolchain etc.Once done, do you want to upload it as PR or shall I do it? Either way is fine with me.

@SethosII
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@sassy-crick Oh, I forgot to change the toolchain to foss/2021a, I corrected it. But feel free to change anything you see fit.

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@SethosII No worries, I was working on that. Did you actually ever manage to install it? I got some problems with tbb and UShER right now.

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@sassy-crick No, I just inserted the version there. What exactly is the issue you have? Can you create a PR for UShER and we try to solve it there?

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@SethosII I uploaded what I have so far to PR 13694

@sassy-crick sassy-crick mentioned this pull request Aug 12, 2021
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I have created a working version for UShER and updated my PR

@sassy-crick
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@SethosII I have a working version for pangolin as well. Happy to share it with you, given you done the ground work for it.
Just let me know.

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@sassy-crick Just create a PR for it yourself. I'm happy as long as there is a working pangolin in EasyBuild ;)

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@SethosII Done. I have created PR 13733 and acknowledge you in the header.

@sassy-crick
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@SethosII Many thanks for your help for this which I do appreciate and apologies for spelling your name wrong!

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@sassy-crick No worries, you're welcome. I'm glad that I could help you.

@SethosII SethosII closed this Aug 28, 2021
@SethosII SethosII deleted the 20210611142001_new_pr_Biopython174 branch September 3, 2021 07:37
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@SethosII @boegelbot @sassy-crick