easyconfig for SearchGUI by korbini · Pull Request #6637 · easybuilders/easybuild-easyconfigs

korbini · 2018-08-06T14:15:54Z

new easyconfig

verdurin · 2018-08-16T09:21:46Z

Hello @korbini and welcome to EasyBuild.

Travis runs some automatic style checks on new PRs to make sure they meet our guidelines. In this case, here's a list of what it's complaining about:

/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:6:121: E501 line too long (298 > 120 characters)
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:22:19: E231 missing whitespace after ','
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:27:1: E101 indentation contains mixed spaces and tabs
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:27:1: W191 indentation contains tabs
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:27:13: E231 missing whitespace after ':'
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:28:1: W191 indentation contains tabs
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:28:19: E231 missing whitespace after ':'
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:29:1: W191 indentation contains tabs
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:29:12: E231 missing whitespace after ':'
/home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb:32:25: E231 missing whitespace after ':'

If you can fix those minor style points, then we'll review the PR.

boegel · 2018-08-16T13:55:47Z

+
+homepage = 'https://github.com/compomics/searchgui'
+description = "SearchGUI runs proteomics identification search engines and de novo sequencing algorithms, currently X! Tandem,
+		MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag."


@korbini You'll need to use """ when wrapping a string across multiple lines.

You can use eb --check-style to make sure your easyconfig matches the style requirements that are checked automatically.

One thing I just noticed: there's no easyblock specified, and there's no custom easyblock for SearchGUI (yet)... Was that omitted by accident maybe?

@boegel Thank you for pointing that out. Hope it's fine now.

boegel · 2018-08-17T10:51:44Z

+
+source_urls = ['http://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/%(version)s/']
+sources = ['SearchGUI-%(version)s-mac_and_linux.tar.gz']
+


@korbini Please include a SHA256 checksum, you can use eb SearchGUI-3.3.3-Java-1.8.0_152.eb --inject-checksums for this.

@boegel
done

boegel · 2018-08-17T10:52:09Z

+    ('Mono', '4.6.2.7')
+]
+
+


@korbini Style nitpicking: please drop the duplicate empty line (same below)

Thank you for the hint. Done.

boegel · 2018-08-17T10:53:01Z

+description = """SearchGUI is a user-friendly open-source graphical user interface for configuring and 
+                 running proteomics identification search engines and de novo sequencing algorithms, 
+                 currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA,
+                 Novor and DirecTag."""


@korbini Better trim the whitespace on these lines to a single space, otherwise this will look quite strange in the output of module show

Thank you for the hint. Done.

boegel · 2018-08-17T10:53:36Z

+
+
+modaliases = {
+    'SearchCLI': 'java -cp $EBROOTSEARCHGUI/SearchGUI-%(version)s.jar eu.isas.searchgui.cmd.SearchCLI',


@korbini Is this using some kind of mirror, or is that just the way how SearchCLI works?

@boegel It looks for me this is like it works, so we found it convenient to give it a version independent alias.
https://compomics.github.io/projects/searchgui/wiki/searchcli.html

boegel · 2018-08-17T10:53:51Z

+    'FastaCLI': 'java -cp $EBROOTSEARCHGUI/SearchGUI-%(version)s.jar eu.isas.searchgui.cmd.FastaCLI'
+}
+
+modextravars = {'LC_ALL': 'C'}


@korbini Can you clarify why this is needed? Not sure that's a good idea...

This is a workaround for MyriMatch on Linux - error “locale::facet::_S_create_c_locale name not valid”, can be fixed by running “export LC_ALL=C” before running SearchGUI/MyriMatch.
Should this be commented in the easyconfig?

korbini

@boegel Changed as requested. Hope it's OK now.

boegel · 2018-08-28T08:14:24Z

+}
+
+modaliases = {
+    'SearchCLI': 'java -cp $EBROOTSEARCHGUI/SearchGUI-%(version)s.jar eu.isas.searchgui.cmd.SearchCLI',


@korbini These aliases are indeed useful, but you should include a comment here to clarify that these are the official command lines, i.e. refer to https://compomics.github.io/projects/searchgui/wiki/searchcli.html

boegel · 2018-08-28T08:15:32Z

+}
+
+# workaround fixing MyriMatch on Linux - error "locale::facet::_S_create_c_locale name not valid"
+modextravars = {'LC_ALL': 'C'}


@korbini This looks like a site-specific fix to me, which means it shouldn't be included in the easyconfig...

How did you trigger the error (so we can test this ourselves to see if we can reproduce it without setting $LC_ALL to C)?

boegel · 2018-09-03T19:04:59Z

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/a7455985da1013c9f0a16716313a1ac5 for a full test report.

boegel · 2018-09-03T19:27:49Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (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/b86cf89cebf3eb9a90d011fb7b3e0255 for a full test report.

boegel · 2018-09-03T19:27:55Z

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/786d41b22c227db2cf0f158f9fa78912 for a full test report.

boegel · 2018-09-03T19:31:23Z

Going in, thanks @korbini!

easyconfig for SearchGUI

b55ed62

boegel added the new label Aug 16, 2018

style fix

d92b570

easybuilders deleted a comment from boegelbot Aug 16, 2018

boegel requested changes Aug 16, 2018

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korbini added 3 commits August 17, 2018 10:49

fix easyblock

1cabd36

Update SearchGUI-3.3.3-Java-1.8.0_152.eb

308a1b0

Update SearchGUI-3.3.3-Java-1.8.0_152.eb

86171f1

boegel requested changes Aug 17, 2018

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boegel reviewed Aug 17, 2018

View reviewed changes

korbini added 3 commits August 17, 2018 14:19

Update SearchGUI-3.3.3-Java-1.8.0_152.eb

610d92a

Update SearchGUI-3.3.3-Java-1.8.0_152.eb

3e710a5

comment style fix

53772bf

korbini commented Aug 28, 2018

View reviewed changes

easybuilders deleted a comment from boegelbot Aug 28, 2018

boegel requested changes Aug 28, 2018

View reviewed changes

extra alias; dropped export LC_ALL=C

40a8c5e

boegel added this to the 3.7.0 milestone Sep 3, 2018

boegel approved these changes Sep 3, 2018

View reviewed changes

boegel changed the base branch from master to develop September 3, 2018 19:31

boegel merged commit a2b5de5 into easybuilders:develop Sep 3, 2018

korbini deleted the patch-1 branch September 4, 2018 07:39


		source_urls = ['http://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/%(version)s/']
		sources = ['SearchGUI-%(version)s-mac_and_linux.tar.gz']



		modaliases = {
		'SearchCLI': 'java -cp $EBROOTSEARCHGUI/SearchGUI-%(version)s.jar eu.isas.searchgui.cmd.SearchCLI',

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korbini commented Aug 6, 2018

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verdurin commented Aug 16, 2018

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korbini Aug 17, 2018 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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boegel commented Sep 3, 2018

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korbini Aug 17, 2018 •

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