{bio}[foss/2018a] KAT v2.4.2 by wpoely86 · Pull Request #6808 · easybuilders/easybuild-easyconfigs

wpoely86 · 2018-09-02T19:24:29Z

(created using eb --new-pr)

… KAT-2.4.2-use-EB-Boost.patch, KAT-2.4.2-fix-python.patch

…into kat * wpoely86/20180902212419_new_pr_KAT242: adding easyconfigs: KAT-2.4.2-foss-2018a-Python-3.6.4.eb and patches: KAT-2.4.2-use-EB-Boost.patch, KAT-2.4.2-fix-python.patch Fix remarks Fix wrong templating in BCALM/2.2.0 Use correct version of BCALM Add easyconfig for BWISE Fix remarks Fix remarks {phys}[foss/2018*] UDUNITS v2.2.26 adding easyconfigs: BCALM-2.2.0-foss-2018a.eb and patches: BCALM-2.2.0-fix-nogit.patch added some extra files to copy added checksums adding easyconfigs: SWIPE-2.1.0-goolf-1.7.20.eb adding easyconfigs: IDBA-UD-1.1.3-foss-2018a.eb add back original patch for TopHat 2.1.1, since it's used in TopHat 2.1.1 easyconfigs update to more recent version of Kent_tools in CIRCexplorer2 easyconfig add missing plus in configopts stick to TopHat 2.1.0 as dependency for CIRCexplorer2 2.3.3, since v2.1.1 results in problems with tophat-reports add missing --with-trio-flavor=netcdf flag to ABINIT 8.x easyconfigs SAMtools 0.1.20 is just a build dep for Cufflinks (since it's statically linked) adding easyconfigs: CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb, TopHat-2.1.1-intel-2018a-Python-2.7.14.eb, Cufflinks-2.2.1-intel-2018a.eb, SAMtools-0.1.20-intel-2018a.eb, segemehl-0.2.0-intel-2018a.eb, pybedtools-0.7.10-intel-2018a-Python-2.7.14.eb

wpoely86 · 2018-09-02T19:38:15Z

Test report by @wpoely86
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
nic1 - Linux centos linux 7.5.1804, AMD Opteron(tm) Processor 6134, Python 2.7.5
See https://gist.github.com/2f81d31315f6a38d1e322d3c40243452 for a full test report.

wpoely86 · 2018-09-03T00:20:46Z

Test report by @wpoely86
FAILED
Build succeeded for 5 out of 8 (6 easyconfigs in this PR)
nic1 - Linux centos linux 7.5.1804, AMD Opteron(tm) Processor 6134, Python 2.7.5
See https://gist.github.com/751c82bc7e0989f850be90d71175c0cc for a full test report.

boegel · 2018-09-03T07:10:23Z

+# Else it will not be able to import scipy
+# Calling Py_setPath before Py_Initialize cause an empty sys.prefix and sys.exec_prefix
+# which makes the site module not search for pth files
+# [email protected]


@wpoely86 worth reporting upstream?

EarlhamInst/KAT#113

boegel · 2018-09-03T07:10:49Z

+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.earlham.ac.uk/kat-tools'
+description = """The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra."""


style nitpicking: just use " rather than """ if it fits on a single line

boegel · 2018-09-03T07:12:26Z

+    ('zlib', '1.2.11'),
+    ('Python', '3.6.4'),
+    ('matplotlib', '2.1.2', versionsuffix),
+    ('Boost', '1.66.0', versionsuffix),


@wpoely86 You'll need to use the new ('Boost.Python', '1.66.0', versionsuffix) (which has regular Boost as a dep) here to make the dependency variant check pass.

boegel · 2018-09-03T07:12:59Z

+
+buildopts = "V=1"
+
+#runtest = "check V=1"


@wpoely86 Why are the tests disabled?

boegel · 2018-09-03T07:13:05Z

+
+preconfigopts = "./autogen.sh && "
+
+buildopts = "V=1"


@wpoely86 Is this still needed?

it's taste, else you don't see what is going on...

We set -DCMAKE_VERBOSE_MAKEFILE=ON for CMakeMake (which implies make V=1), we should to the same for ConfigureMake rather than only do it for some easyconfigs?

boegel · 2018-09-03T07:13:30Z

+
+#runtest = "check V=1"
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && DESTDIR=/ "


the DESTDIR=/ looks weird, what's up with that?

It's bio-informatics, do I really need to clarify? 😉

The issue is here: https://github.com/TGAC/KAT/blob/master/scripts/Makefile.am#L32

Just clarify with a comment, it looks weird, something like this:

# (explain here) preinstallopts += " && DESTDIR=/ "

boegel · 2018-09-03T07:13:43Z

@@ -0,0 +1,70 @@
+diff -ur KAT-Release-2.4.2.orig/lib/Makefile.am KAT-Release-2.4.2/lib/Makefile.am


@wpoely86 missing description + author

boegel · 2018-09-03T07:14:21Z

        'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'],
        'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'],
    }),
+    ('tabulate', '0.8.2', {


@wpoely86 Please open a separate PR for this, and make this consistent for all (non-bare) Python 3.6.4 easyconfigs + all more recent (3.x) versions.

@wpoely86 This PR can't go in until we have a PR merged that adds tabulate to all recent Python 3.x easyconfigs...

The rest goes in a separate PR

wpoely86 · 2018-09-03T10:30:14Z

Test report by @wpoely86
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in this PR)
nic157 - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz, Python 2.7.5
See https://gist.github.com/eeb5137b9214d3d3152f79fa1ff885cd for a full test report.

boegel · 2018-09-03T11:54:47Z

@wpoely86 PR #6809 is now merged, please sync this PR (and look into a new test report?)

* origin/develop: Add tabulate extension to all Python > 3.6 easyconfigs

wpoely86 · 2018-09-03T12:03:40Z

Test report by @wpoely86
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
nic157 - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz, Python 2.7.5
See https://gist.github.com/1684cc57774cc173b4a520cda8bd4279 for a full test report.

boegel · 2018-09-03T13:58:06Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2418.golett.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/a514bdb0245a2741b8ff3aacde9586ca for a full test report.

boegel · 2018-09-03T13:59:28Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2002.delcatty.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/1cccc8237e968a88ed2dd2dae8b529ca for a full test report.

boegel · 2018-09-03T14:01:51Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in this PR)
node3126.skitty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 2.7.5
See https://gist.github.com/072176d70183c19873a956b9dd1b07b1 for a full test report.

boegel · 2018-09-03T14:02:06Z

Going in, thanks @wpoely86!

wpoely86 and others added 2 commits September 1, 2018 15:34

Add tabulate/0.8.2 to Python/3.6.4

e3c8132

adding easyconfigs: KAT-2.4.2-foss-2018a-Python-3.6.4.eb and patches:…

cb9cbf6

… KAT-2.4.2-use-EB-Boost.patch, KAT-2.4.2-fix-python.patch

wpoely86 added the new label Sep 2, 2018

wpoely86 requested a review from boegel September 2, 2018 19:43

boegel reviewed Sep 3, 2018

View reviewed changes

boegel requested changes Sep 3, 2018

View reviewed changes

wpoely86 added 2 commits September 3, 2018 09:44

Fix remarks

72855ba

Only changed the needed Python easyconfig

228bf8d

The rest goes in a separate PR

easybuilders deleted a comment from boegelbot Sep 3, 2018

boegel added this to the 3.7.0 milestone Sep 3, 2018

wpoely86 added 2 commits September 3, 2018 13:56

Merge remote-tracking branch 'origin/develop' into kat

077274b

* origin/develop: Add tabulate extension to all Python > 3.6 easyconfigs

Fix checksum

33532b2

boegel approved these changes Sep 3, 2018

View reviewed changes

boegel merged commit 61ff90f into easybuilders:develop Sep 3, 2018

wpoely86 deleted the 20180902212419_new_pr_KAT242 branch September 3, 2018 14:04


		#runtest = "check V=1"

		preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && DESTDIR=/ "

		@@ -0,0 +1,70 @@
		diff -ur KAT-Release-2.4.2.orig/lib/Makefile.am KAT-Release-2.4.2/lib/Makefile.am


		preconfigopts = "./autogen.sh && "

		buildopts = "V=1"

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wpoely86 commented Sep 3, 2018

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