{bio}[foss/2016b] HiC-Pro v2.9.0, bx-python v0.7.4 by timeu · Pull Request #5873 · easybuilders/easybuild-easyconfigs

timeu · 2018-02-21T15:25:42Z

(created using eb --new-pr)

…hon-0.7.4-foss-2016b-Python-2.7.12.eb

verdurin · 2018-02-22T23:12:28Z

+    ('python-lzo', '1.11', {
+        'modulename': 'lzo',
+        'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'],
+        'source_tmpl': 'python-lzo-%(version)s.tar.gz',


@timeu - please add checksums for the extensions with --inject-checksums.

verdurin · 2018-02-22T23:12:54Z

+toolchain = {'name': 'foss', 'version': '2016b'}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/nservant/HiC-Pro/archive/']


@timeu please add an SHA256 checksum.

verdurin · 2018-02-25T22:07:28Z

+
+toolchain = {'name': 'foss', 'version': '2016b'}
+
+


@timeu - please remove this unnecessary extra blank line

verdurin · 2018-02-25T22:08:29Z

+sources = ['v%(version)s.tar.gz']
+checksums = ['b82f15747bce937c3337b8120ad331a4bc07bbed6708d1d38b7d6ff1047a7a81']
+
+# buildopts=" configure" 


@timeu - any reason why this comment is still here? Something you found during testing?

no I think it was an artifact from a copy. I will remove it.

boegel · 2018-04-24T18:53:35Z

+skipsteps = ['configure']
+
+files_to_copy = [
+    (['scripts'], ''),


@timeu This looks odd... What's the point of this in combination with the line below?

hmm good question, I guess the line below is redundant. I can remove it

You should change this entry to just 'scripts' imho...

boegel · 2018-04-24T19:01:25Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in this PR)
node2121.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/0b19f88792aebe868b17746c6e181855 for a full test report.

boegel · 2018-05-23T11:07:42Z

+
+exts_defaultclass = 'PythonPackage'
+
+patches = ['HiC-Pro.patch']


@timeu Please rename the patch to something like HiC-Pro-2.9l0_eb.patch, and move this up between sources = and checksums =

boegel · 2018-05-23T11:08:06Z

+skipsteps = ['configure']
+
+files_to_copy = [
+    ('scripts'),


you can drop the (...) here?

boegel · 2018-05-23T11:08:22Z

+files_to_copy = [
+    ('scripts'),
+    (['bin/utils', 'bin/HiC-Pro'], 'bin'),
+    (['config-system.txt'], '')


this is equivalent with just using 'config-system.txt'?

boegel · 2018-05-23T11:12:30Z

+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'bin/utils'],
+}
+
+postinstallcmds = [


this should be moved up, below files_to_copy (order doesn't matter in an easyconfig file, but style-wise we try to keep easyconfig parameter more-or-less in order of execution)

boegel · 2018-05-23T11:13:01Z

@@ -0,0 +1,34 @@
+diff -ruN HiC-Pro-2.9.0/config-system.txt HiC-Pro-2.9.0-patched/config-system.txt


@timeu Please include a short description of the patch above this line, and mention the author (or include a reference to where you got the patch from)

@timeu Please remove this old (now unused) patch?

boegel · 2018-07-06T08:58:05Z

@timeu ping?

timeu · 2018-07-06T09:01:28Z

@boegel Sorry for the delay. I will take care of the remaining issues today.

boegel · 2018-08-14T07:57:53Z

@@ -0,0 +1,34 @@
+diff -ruN HiC-Pro-2.9.0/config-system.txt HiC-Pro-2.9.0-patched/config-system.txt


@timeu Please remove this old (now unused) patch?

suggestions are implemented now

boegel · 2018-08-23T17:10:23Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
node2594.golett.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/f03d6e7cf445bce5d9fb791e241861ce for a full test report.

boegel · 2018-08-23T19:10:49Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
node2015.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/ff903bf21223694d9f36ccc5ddcc87cf for a full test report.

boegel · 2018-08-23T19:12:08Z

Going in, thanks @timeu!

adding easyconfigs: HiC-Pro-2.9.0-foss-2016b-Python-2.7.12.eb, bx-pyt…

7e2dd0e

…hon-0.7.4-foss-2016b-Python-2.7.12.eb

verdurin requested changes Feb 22, 2018

View reviewed changes

Added checksums

2b38ed7

verdurin added this to the 3.5.2 milestone Feb 25, 2018

verdurin previously requested changes Feb 25, 2018

View reviewed changes

boegel modified the milestones: 3.5.2, 3.6.0 Feb 26, 2018

Removed blank line and comment

532d614

boegel reviewed Apr 24, 2018

View reviewed changes

boegel added new update labels Apr 24, 2018

boegel modified the milestones: 3.6.0, next release Apr 24, 2018

Added patch for HiC-Pro and fixed copy directive

7cf6bc6

boegel requested changes May 23, 2018

View reviewed changes

boegel modified the milestones: 3.6.1, next release May 23, 2018

boegel modified the milestones: 3.6.2, next release Jul 6, 2018

Addressed reviewers comments

a1324cd

boegel requested changes Aug 14, 2018

View reviewed changes

Delete unused patch file

57816aa

boegel approved these changes Aug 23, 2018

View reviewed changes

boegel merged commit e711794 into easybuilders:develop Aug 23, 2018


		exts_defaultclass = 'PythonPackage'

		patches = ['HiC-Pro.patch']

		@@ -0,0 +1,34 @@
		diff -ruN HiC-Pro-2.9.0/config-system.txt HiC-Pro-2.9.0-patched/config-system.txt

Conversation

timeu commented Feb 21, 2018

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

boegel Apr 24, 2018 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

boegel commented Apr 24, 2018

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

boegel commented Jul 6, 2018

Uh oh!

timeu commented Jul 6, 2018

Uh oh!

Choose a reason for hiding this comment

Uh oh!

boegel commented Aug 23, 2018

Uh oh!

boegel commented Aug 23, 2018

Uh oh!

boegel commented Aug 23, 2018

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

boegel Apr 24, 2018 •

edited

Loading