{bio}[foss/2016b] GroopM 0.3.4 w/ Python 2.7.12 + deps by manifestoso · Pull Request #4650 · easybuilders/easybuild-easyconfigs

manifestoso · 2017-05-31T09:07:39Z

{bio}[foss/2016b] GroopM and deps

boegel · 2017-05-31T15:06:00Z

@robqiao For foss/2016b, you may want to stick to Python 2.7.12?

boegel · 2017-05-31T15:07:22Z

+    ('Python', '2.7.13'),
+    ('Cython', '0.25.2', versionsuffix),
+    ('numpy', '1.11.1', versionsuffix),
+    ('scipy', '0.17.1', versionsuffix),


@robqiao Python already includes both numpy and scipy, if those versions are recent enough there's no reason to include stand-alone installations for them as dependencies?

@boegel This package is compiled against specific numpy and scipy version, any suggestions?

Can you clarify? How exactly does it require these specific versions of numpy/scipy?

@boegel Sorry, my fault, version for numpy and scipy are correct in Python/2.7.12-foss-2016b

…-easyconfigs into addeasyconfigs

manifestoso · 2017-06-08T02:06:36Z

@boegel merge this PR?

boegel · 2017-06-08T08:01:02Z

+exts_filter = ("python -c 'import %(ext_name)s'", '')
+
+exts_list = [
+    ('pysam', version, {


@robqiao Why is this being installed as a bundle when there's only one extension?

It should just be installed via PythonPackage directly, like in https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb?

It makes sense to do it as a bundle if you include Cython as an extension in the Pysam installation, but that's not done here?

boegel · 2017-06-08T08:01:57Z

+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'],


this is quite specific, and may cause trouble on some system, we usually just check for lib/python%(pyshortver)s/site-packages, which suffices since it's combined with the import check done by EasyBuild

boegel · 2017-06-08T08:02:10Z

+
+toolchain = {'name': 'foss', 'version': '2016b'}
+
+parallel = 1


this can be removed?

boegel · 2017-06-08T08:02:58Z

+dependencies = [
+    ('Python', '2.7.12'),
+    ('numexpr', '2.6.1', versionsuffix),
+    ('HDF5', '1.8.18'),


existing PyTables easyconfigs also include LZO and Blosc as dependencies?

Now included: LZO, BLOSC

boegel · 2017-06-08T08:03:45Z

+ relatively short nucleotide sequences against a long reference sequence such as the human genome."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'optarch': True, 'pic': True, 'usempi': True}


existing BWA easyconfigs don't enable usempi, so it's not needed?

You are right.

…nto addeasyconfigs

…onfigs into addeasyconfigs

…-easyconfigs into addeasyconfigs

manifestoso · 2017-08-04T08:38:18Z

@verdurin do you mind to run checks on this PR again? Thx ;)

verdurin · 2017-08-06T07:25:58Z

Test report by @verdurin
FAILED
Build succeeded for 21 out of 25 (18 easyconfigs in this PR)
ca005.camp.thecrick.org - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/68694a7a90a753978fab6659cb094d7e for a full test report.

boegel · 2017-08-07T09:46:01Z

+]
+
+builddependencies = [
+    ('Automake', '1.11.3'),


@robqiao Can you clarify the need for using an old version of Automake here?

Also, you're adding two versions of both Automake and Autoconf (as a dep to Automake), but using only one of them, so remove the others to clean up the PR a bit?

@robqiao yes, I did spot quite a bit of duplication during my failed build attempt yesterday, so I echo the comment by @boegel

@boegel @verdurin Thanks guys for pointing out. BamM-1.7.3 distribution can only be built by specific Automake/Autoconf version, we have filed the issue, but until we get an update on this, stick to those versions is the safest bet.
I have other files that require additional Automake/Autoconf versions, but I guess I can clean up for the time being and includes in the corresponding pr.

boegel · 2017-08-07T09:47:47Z

+source_urls = ['https://github.com/macroevolution/bamm/archive']
+sources = ['v%(version)s.tar.gz']
+
+checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4', 'sha256']


this is wrong, should be either:

checksums = [('526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4', 'sha256')]

or

checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4']

I suggest the latter, where eb detects the checksum type automatically to be SHA256 based on the length, as we do elsewhere.

@boegel Thanks for the tips. Fixed tuple() obj.

boegel · 2017-08-07T09:48:49Z

+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
+
+checksums = ['fcf470a46a1dbe2f96a1c5b87c530554', 'md5']


please use a SHA256 checksum instead, and drop the md5, this doesn't do what you think (it specifies a 2nd checksum md5, which is never used, rather than specifying the checksum type of the provided checksum value), see also other remark

boegel · 2017-08-07T09:49:12Z

+source_urls = ['https://github.com/Blosc/c-blosc/archive/']
+sources = ['v%(version)s.tar.gz']
+
+checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8', 'sha256']


please drop the sha256, see also other remark

boegel · 2017-08-07T09:49:24Z

+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [homepage + 'download/']
+
+checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072', 'sha256']


please drop the sha256, see also other remark

boegel · 2017-08-07T11:07:16Z

Test report by @boegel
SUCCESS
Build succeeded for 18 out of 18 (18 easyconfigs in this PR)
node2573.golett.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/8acb0c2e0c2487f7a61aefecce755928 for a full test report.

manifestoso · 2017-08-11T02:24:09Z

@boegel Thanks for the tips. do you mind to check this pr again? Thx

…lders#4650

boegel · 2017-08-12T09:09:22Z

We're working towards requiring SHA256 checksums for sources/patches in all easyconfigs touched in pull requests (see #5001), so I went through the trouble of adding the missing ones here, see manifestoso#1 (if you merge that PR, your PR here will be updated accordingly).

I'm looking into adding support for something like eb --add-checksums=sha256 foo.eb to make including checksums less painful..

consistently add SHA256 checksums for easyconfigs added in PR easybuilders#4650

manifestoso · 2017-08-12T14:39:19Z

@boegel --add-checksums will be awesome. But what's the checking mechanism will be like? If the check is only based on the URL provided by source_urls, malicious package can also been introduced, unless the purpose of the check is really to stop the man in the middle attack?

boegel · 2017-08-12T14:49:15Z

Test report by @boegel
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in this PR)
node2432.golett.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/fac0a413c3facc8b2cb5d73318ea267f for a full test report.

boegel · 2017-08-12T14:57:30Z

Test report by @boegel
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in this PR)
node2040.delcatty.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/ee9e468fbf2a5b8af159c6f16e0cc0c9 for a full test report.

remarks tackled

boegel · 2017-09-06T21:46:50Z

Going in, thanks @robqiao!

Robert and others added 5 commits May 31, 2017 18:35

{bio}[foss/2016b] GroopM and deps

ecdd4e4

file name fixed

ec8852a

numpy added

d4ab52d

Merge branch 'addeasyconfigs' of https://github.com/robqiao/easybuild…

1938e02

…-easyconfigs into addeasyconfigs

SAMtools added

d9b6a9c

boegel reviewed May 31, 2017

View reviewed changes

Robert and others added 10 commits June 1, 2017 19:19

Pysam added

6dbb79f

BamM Python ext updated

4906595

Python ext updated

43d1358

Merge branch 'addeasyconfigs' of https://github.com/robqiao/easybuild…

c7d2260

…-easyconfigs into addeasyconfigs

GroopM deps version updated

274d6e6

GroopM version updated

2076bf7

PyTable Python version updated

effafc9

deps version updated

9a666f0

matplotlib1.5.2 removed

ea91b85

deps version updated

ad02967

boegel requested changes Jun 8, 2017

View reviewed changes

Robert and others added 11 commits July 26, 2017 12:15

Merge branch 'develop' of github.com:hpcugent/easybuild-easyconfigs i…

3694281

…nto addeasyconfigs

GRIDSS easyconfig added

d4ef20f

GRIDSS removed

a594817

erratum

cf13cea

more deps added

38e5a51

Merge branch 'develop' of https://github.com/hpcugent/easybuild-easyc…

1de55ba

…onfigs into addeasyconfigs

Merge branch 'addeasyconfigs' of https://github.com/robqiao/easybuild…

d48fe77

…-easyconfigs into addeasyconfigs

erratum

43185b8

formatting error

319aab5

formatting error correction

0ead132

format error correction

9036bcf

Robert Qiao added 3 commits August 4, 2017 08:16

libunistring-0.9.7-GCCcore-6.4.0.eb restored

39bfe18

util-linux-2.30-GCCcore-6.4.0.eb restored

8df4310

BamM style erratum

063c7e7

boegel requested changes Aug 7, 2017

View reviewed changes

Robert Qiao added 2 commits August 8, 2017 12:38

checksum style fixed

069e22e

Autoconf/Automake version cleanup

c02f91f

easybuilders deleted a comment from boegelbot Aug 12, 2017

boegel changed the title ~~{bio}[foss/2016b] GroopM~~ {bio}[foss/2016b] GroopM 0.3.4 w/ Python 2.7.12 + deps Aug 12, 2017

consistently add SHA256 checksums for easyconfigs added in PR easybui…

e9a7d31

…lders#4650

boegel mentioned this pull request Aug 12, 2017

consistently add SHA256 checksums for easyconfigs added in PR #4650 manifestoso/easybuild-easyconfigs#1

Merged

Merge pull request #1 from boegel/addeasyconfigs

889d125

consistently add SHA256 checksums for easyconfigs added in PR easybuilders#4650

boegel approved these changes Sep 6, 2017

View reviewed changes

boegel merged commit 3a0f9e7 into easybuilders:develop Sep 6, 2017

manifestoso deleted the addeasyconfigs branch September 10, 2017 02:07


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

		parallel = 1

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