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fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure step to be after installation#15280

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wdlingit:15279_repeatmasker_config_after_install
Jun 4, 2022
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fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure step to be after installation#15280
Micket merged 2 commits intoeasybuilders:developfrom
wdlingit:15279_repeatmasker_config_after_install

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@wdlingit wdlingit commented Apr 14, 2022 •
edited by boegel
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fixes #15279

The change is simply to run the configure script at the installdir but not builddir. After installing, the builddir will be missing, and the path pointing to builddir (saved in the configure step) will become invalidate. Just like the steps described by RepeatMasker download page, the configure script is executed at where it was installed.

@wdlingit wdlingit changed the title #15279 make configure step at the installdir {bio}[foss-2020b] RepeatMasker-4.1.2-p1 Apr 15, 2022
verdurin
verdurin requested changes Apr 19, 2022
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Comment thread easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb
@boegel boegel added the bug fix label Apr 19, 2022
@boegel boegel added this to the next release (4.5.5?) milestone Apr 19, 2022
@wdlingit wdlingit changed the title {bio}[foss-2020b] RepeatMasker-4.1.2-p1 fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure step to be after installation Apr 20, 2022
@wdlingit wdlingit requested review from boegel and verdurin April 20, 2022 07:06
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boegel commented Jun 4, 2022

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3502.doduo.os - Linux RHEL 8.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/2771f4c1f91177484b71c483ecc039f1 for a full test report.

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boegelbot commented Jun 4, 2022

@wdlingit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/2440016355
Output from first failing test suite run:

FAIL: test_style_conformance (test.easyconfigs.styletests.StyleTest)
Check the easyconfigs for style
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/styletests.py", line 68, in test_style_conformance
    self.assertEqual(result, 0, error_msg)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/base/testing.py", line 116, in assertEqual
    raise AssertionError("%s:\nDIFF%s:\n%s" % (msg, limit, ''.join(diff[:self.ASSERT_MAX_DIFF])))
AssertionError: There shouldn't be any code style errors (and/or warnings), found 4:
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb:39:1: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb:40:1: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb:41:1: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb:48:20: E201 whitespace after '['

: 4 != 0:
DIFF:
- 4

----------------------------------------------------------------------
Ran 14820 tests in 708.236s

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

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@boegel boegel mentioned this pull request Jun 4, 2022
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boegel commented Jun 4, 2022

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3108.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/fb9d32ef79627659a23d7372a95d520c for a full test report.

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boegel commented Jun 4, 2022

Trivial code style issues that are making tests fail are fixed in #15615

@Micket Micket merged commit a1c34f0 into easybuilders:develop Jun 4, 2022
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RepeatMasker-4.1.2-p1 configure step should be in installdir

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