{bio}[intel/2017a] EvidentialGene 2018.01.01 (REVIEW) by hajgato · Pull Request #5627 · easybuilders/easybuild-easyconfigs

hajgato · 2018-01-12T12:36:36Z

No description provided.

verdurin · 2018-01-18T10:07:15Z

@@ -0,0 +1,39 @@
+easyblock = "PackedBinary"
+
+name = "EvidentalGene"


@hajgato - the name should be EvidentialGene, surely?

@verdurin For me it can be anything, its hard to figure it out what to give. The homepage references many times to EvidentalGene as well as evigene.

@verduin I must be blind. Typo corrected.

verdurin · 2018-01-18T10:08:34Z

+month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec']
+dlver = version.split('.')[0][-2:]
+dlver += month[int(version.split('.')[1])]
+dlver += version.split('.')[2]


Oof. What a mither...

verdurin · 2018-01-18T10:09:20Z

+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/']
+sources = [SOURCELOWER_TAR_GZ]


Please add a checksum here.

@verdurin Done

verdurin

Thanks for the fixes @hajgato

verdurin · 2018-02-09T18:09:01Z

Test report by @verdurin
SUCCESS
Build succeeded for 5 out of 5 (2 easyconfigs in this PR)
rescomp2 - Linux centos 6.8, Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz, Python 2.7.11
See https://gist.github.com/84c82c23b2bd9955305950e41fb0b88e for a full test report.

boegel · 2018-02-11T09:18:26Z

+dlver = version.split('.')[0][-2:]
+dlver += month[int(version.split('.')[1])]
+dlver += version.split('.')[2]
+sources = ['evigene%s.tar' % dlver]


Ugh, this is a bit messy, creative versioning, yaay!

I would propose to clean this up a little bit:

month = ['jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] dlver = '%(version_major)s'[-2:] + month[int('%(version_minor)s') - 1] + version.split('.')[2]

boegel · 2018-02-11T09:19:51Z

+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = ['ftp://arthropods.eugenes.org/evigene_old/']


URL is wrong? Also, prefer http over ftp when possible.

http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/

url is not wrong, for me it works. but http used.

boegel · 2018-02-11T09:19:59Z

+
+name = "EvidentialGene"
+version = '2018.01.01'
+


style nitpicking: please drop this empty line

boegel · 2018-02-11T09:20:29Z

+checksums = ['6972108112cdb1fb106da11321d06b09f518b544e4739d0bf19da1984131e221']
+
+dependencies = [
+    ('Perl', '5.24.1', '', ('GCCcore', '6.3.0')),


Why hardcode to GCCcore/6.3.0 subtoolchain, there's no need to?

wanted to be sure that the GCCcore version is used. (we have Intel version as well)

hajgato · 2018-02-12T08:44:11Z

@boegel Style fixes + http + hardcoded GCCcore Perl fixed.

boegel · 2018-02-25T11:26:22Z

+    'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/',
+]
+month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec']
+dlver = '%(version_major)s'[-2:] + month[int('%(version_minor)s') - 1] + version.split('.')[2]


@hajgato This doesn't work, it breaks parsing of the easyconfig file:

Parsing easyconfig file failed: invalid literal for int() with base 10: '%(version_minor)s' (line 21)"

The template values can only be replaced after parsing the easyconfig file, so the int(...) is getting a literal '%(version_minor)s string...

@boegel Fixed

boegel · 2018-02-26T20:44:45Z

+    'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/',
+]
+month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec']
+dlver = '%(version_major)s'[-2:] + month[int(version.split('.')[1])] + version.split('.')[2]


@hajgato The '%(version_major)s'[-2:] prematurely resolves to )s, which doesn't work either...

You'll need to replace it with version.split('.')[0][-2:]?

hajgato · 2018-02-27T08:06:00Z

@boegel decided to go back to the original dlver

boegel · 2018-02-27T12:50:05Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
node2689.swalot.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/b0d54d199abc10e0045aa2dc635630fd for a full test report.

boegel · 2018-02-27T12:52:54Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
node2030.delcatty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/9fcba323dba65c627e491e68c688892c for a full test report.

boegel · 2018-02-27T14:18:40Z

Going in, thanks @hajgato!

{bio}[intel/2017b] EvidentalGene 2018.01.01 (REVIEW)

079a985

verdurin added this to the next release (3.5.2 or 3.6.0) milestone Jan 18, 2018

verdurin requested changes Jan 18, 2018

View reviewed changes

Balazs Hajgato added 2 commits January 18, 2018 11:36

Checksum injected

5be591d

Typo corrected

9d11e33

verdurin previously approved these changes Feb 9, 2018

View reviewed changes

boegel requested changes Feb 11, 2018

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boegel added new update labels Feb 11, 2018

Style fixes

8475dff

hajgato dismissed verdurin’s stale review via 8475dff February 12, 2018 08:43

hajgato changed the title ~~{bio}[intel/2017a] EvidentalGene 2018.01.01 (REVIEW)~~ {bio}[intel/2017a] EvidentialGene 2018.01.01 (REVIEW) Feb 21, 2018

boegel requested changes Feb 25, 2018

View reviewed changes

boegel modified the milestones: 3.5.2, 3.x Feb 25, 2018

month fixed

9ccd3ba

boegel requested changes Feb 26, 2018

View reviewed changes

Go back to original dlver

3055b35

boegel approved these changes Feb 27, 2018

View reviewed changes

boegel modified the milestones: 3.x, 3.5.2 Feb 27, 2018

boegel merged commit 5cc757d into easybuilders:develop Feb 27, 2018

		@@ -0,0 +1,39 @@
		easyblock = "PackedBinary"

		name = "EvidentalGene"


		toolchain = {'name': 'intel', 'version': '2017a'}

		source_urls = ['ftp://arthropods.eugenes.org/evigene_old/']

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hajgato commented Jan 12, 2018

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verdurin commented Feb 9, 2018

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hajgato commented Feb 12, 2018

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hajgato commented Feb 27, 2018

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boegel commented Feb 27, 2018

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