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The test suite that is available in 'medata/test' in https://github.com/nanoporetech/medaka, which you can run with 'pytest medaka', passes fully (189 tests passed, no errors/failures).
I can't run the tests in the easyconfig though, since 'medaka/test' is not included in the release provided on PyPI, and using the sources straight from GitHub is not an option either since then the files in medaka/data are just stubs rather than the actual files (which are pulled in with git-lfs on 'git clone')... See also the discussion in nanoporetech/medaka#125.
Test report by @boegel SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/74e1024df5f2fe22468e0e9e6b3598b8 for a full test report.
Test report by @boegel SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2463.golett.os - Linux centos linux 7.7.1908, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/31403573c91a4c773609dc1c8be00e06 for a full test report.
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(created using
eb --new-pr)I'm forced to use an older toolchain here, since the latest version of medaka has some fairly strict version requirements, i.e.:
(see also How strict are the version requirements for dependencies? nanoporetech/medaka#124 and Support for python >=3.7 nanoporetech/medaka#123)
The test suite that is available in 'medata/test' in https://github.com/nanoporetech/medaka, which you can run with 'pytest medaka', passes fully (189 tests passed, no errors/failures).
I can't run the tests in the easyconfig though, since 'medaka/test' is not included in the release provided on PyPI, and using the sources straight from GitHub is not an option either since then the files in medaka/data are just stubs rather than the actual files (which are pulled in with git-lfs on 'git clone')... See also the discussion in nanoporetech/medaka#125.