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{bio}[foss/2018b] limix v2.0.4, bgen-reader v3.0.2 w/ Python v3.6.6 plus dependencies#11867

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lexming:wrapper7456
Dec 21, 2020
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{bio}[foss/2018b] limix v2.0.4, bgen-reader v3.0.2 w/ Python v3.6.6 plus dependencies#11867
boegel merged 28 commits intoeasybuilders:developfrom
lexming:wrapper7456

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@lexming lexming commented Dec 11, 2020 •
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Wrapper PR for #7456

I have cleaned up quite thoroughly the PR, using as much dependencies from the tree as possible.

Completetly new easyconfigs:

  • limix-2.0.4-foss-2018b-Python-3.6.6.eb
  • bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb
  • liknorm-1.5.2-GCCcore-7.3.0.eb
  • logaddexp-1.0.3-GCCcore-7.3.0.eb
  • chi2comb-0.0.3-GCCcore-7.3.0.eb

New easyconfigs with other versions already in tree:

  • almosthere-1.0.1-GCCcore-7.3.0.eb
  • bgen-3.0.2-GCCcore-7.3.0.eb
  • cytoolz-0.10.1-foss-2018b-Python-3.6.6.eb
  • netcdf4-python-1.4.1-foss-2018b-Python-3.6.6.eb
  • numba-0.39.0-foss-2018b-Python-3.6.6.eb
  • statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb
  • xarray-0.12.1-foss-2018b-Python-3.6.6.eb
  • zstd-1.4.0-GCCcore-7.3.0.eb

Moreover, I also updated a couple of existing easyconfigs in the tree

  1. rename the existing easyconfig limix-bgen to bgen. limix is the name of the developer, not the software and there are no other bgen packages that could cause confusion.
  2. I'm also making some minor changes to almosthere-1.0.10-GCCcore-9.3.0.eb to standarize all easyconfigs of almosthere.

easybuild@GMI and others added 13 commits January 21, 2019 09:38
adding easyconfigs: almosthere-1.0.1-GCCcore-7.3.0.eb, bgen-3.0.2-fos…
aebdb77 
…s-2018b.eb, bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb, cftime-1.0.1-foss-2018b-Python-3.6.6.eb, limix-2.0.1-foss-2018b-Python-3.6.6.eb, lz4-1.8.3-GCCcore-7.3.0.eb, netcdf4-python-1.4.1-foss-2018b-Python-3.6.6.eb, statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb, zstd-1.3.8-foss-2018b.eb
Add missing dependencies
49fb6bc
Fix issues
f041398
Fix reviewers comments
a3c09ad
@timeu
Delete liknorm-1.4.6-foss-2018b.eb
3999136
@timeu
Delete zstd-1.3.8-foss-2018b.eb
3dfd64e
Fix issues
efeb2a6
Fix issues
52c80e2
Fix issues
eaaed12
@lexming
use netcdf4-python v1.4.3 in limix-2.0.1-foss-2018b-Python-3.6.6.eb
9fdfbca
@lexming
use distributed from dask v0.19.4 in limix-2.0.1-foss-2018b-Python-3.…
9f2f818 
…6.6.eb
@lexming
remove duplicate of lz4-1.8.3-GCCcore-7.3.0.eb
1568347
@lexming
Merge branch 'develop' of github.com:easybuilders/easybuild-easyconfi…
66a484c 
…gs into wrapper7456
@easybuilders easybuilders deleted a comment from boegelbot Dec 12, 2020
@lexming lexming added this to the 4.x milestone Dec 12, 2020
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Comment thread easybuild/easyconfigs/a/almosthere/almosthere-1.0.1-GCCcore-7.3.0.eb Outdated
Comment thread easybuild/easyconfigs/x/xarray/xarray-0.12.1-foss-2018b-Python-3.6.6.eb Outdated
Comment thread easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-3.6.6.eb Outdated
lexming added 11 commits December 13, 2020 00:24
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@easybuilders easybuilders deleted a comment from boegelbot Dec 13, 2020
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lexming commented Dec 13, 2020

Test report by @lexming
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in total)
node379.hydra.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 2.7.5
See https://gist.github.com/de1acb0550998f8d2e8028c747b47c34 for a full test report.

@lexming lexming changed the title {bio}[foss/2018b] limix v2.0.1 w/Python v3.6.6 plus dependencies {bio}[foss/2018b] limix v2.0.4, bgen-reader v3.0.2 w/ Python v3.6.6 plus dependencies Dec 13, 2020
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zao commented Dec 13, 2020

Test report by @zao
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
eb-u1604 - Linux ubuntu 16.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 2.7.12
See https://gist.github.com/6644b3f081a253b28a08b02d2c91c4cc for a full test report.

@branfosj branfosj mentioned this pull request Dec 13, 2020
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lexming commented Dec 13, 2020

Depends on #11873 , which fixes failed test in #11867 (comment)

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zao commented Dec 13, 2020

Test report by @zao
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in total)
eb-u1604 - Linux ubuntu 16.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 2.7.12
See https://gist.github.com/c7ab5442a37484fa9270fe3fda97cdc5 for a full test report.

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zao commented Dec 13, 2020

The successful test report of mine above was made with the fixed LLVM.

boegel
boegel approved these changes Dec 21, 2020
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lgtm, more test reports coming in...

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boegel commented Dec 21, 2020

Test report by @boegel
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in total)
node3607.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/dd9618601f306c206d781b50432160de for a full test report.

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boegel commented Dec 21, 2020

Test report by @boegel
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in total)
node3106.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/70cd7b1957e3821abe53ab7151bd3edf for a full test report.

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boegel commented Dec 21, 2020

Test report by @boegel
SUCCESS
Build succeeded for 16 out of 16 (16 easyconfigs in total)
node2658.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/bfcbb3a5fdc0aff224a0bfa3b7a90b2f for a full test report.

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boegel commented Dec 21, 2020

Going in, thanks @lexming!

@boegel boegel merged commit 5149823 into easybuilders:develop Dec 21, 2020
@boegel boegel modified the milestones: 4.x, next release (4.3.3?) Dec 21, 2020
@lexming lexming deleted the wrapper7456 branch December 21, 2020 16:16
@lexming lexming mentioned this pull request Dec 21, 2020
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