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{bio}[foss/2019a] FSL v6.0.1#8896

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boegel merged 5 commits intoeasybuilders:developfrom
vanzod:20190911093100_new_pr_FSL601
Sep 17, 2019
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{bio}[foss/2019a] FSL v6.0.1#8896
boegel merged 5 commits intoeasybuilders:developfrom
vanzod:20190911093100_new_pr_FSL601

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@vanzod vanzod commented Sep 11, 2019

(created using eb --new-pr)

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adding easyconfigs: FSL-6.0.1-foss-2019a-Python-2.7.15.eb, FSL-6.0.1-…
0743f99 
…foss-2019a-Python-3.7.2.eb and patches: FSL-6.0.1_Build_extras.patch, FSL-6.0.1_Makefile_fixes.patch, FSL-6.0.1_Melodic-use-ifstream-good.patch
@vanzod vanzod added the update label Sep 11, 2019
@vanzod vanzod added this to the 4.x milestone Sep 11, 2019
@easybuilders easybuilders deleted a comment from boegelbot Sep 11, 2019
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vanzod commented Sep 11, 2019

Test report by @vanzod
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
cermis - Linux debian 9.9, Intel(R) Xeon(R) CPU X5670 @ 2.93GHz, Python 2.7.13
See https://gist.github.com/7b84b37aa61b256199f4a21b50fa7abd for a full test report.

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verdurin commented Sep 12, 2019

Test report by @verdurin
FAILED
Build succeeded for 18 out of 22 (5 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.6.1810, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/452d364111bb9102b3fd592df161416b for a full test report.

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verdurin commented Sep 12, 2019

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (5 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.6.1810, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/e772111a72b49ef4bee92b0de3acdcbb for a full test report.

@vanzod vanzod added the new label Sep 12, 2019
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verdurin commented Sep 13, 2019

@vanzod Does this have fixes for #7899 ?

boegel
boegel previously approved these changes Sep 14, 2019
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lgtm

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boegel commented Sep 14, 2019

Test report by @boegel
SUCCESS
Build succeeded for 6 out of 6 (5 easyconfigs in this PR)
node3110.skitty.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 2.7.5
See https://gist.github.com/5e6ff40c92456ee09b8a27a52b111bbe for a full test report.

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boegel commented Sep 14, 2019

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (5 easyconfigs in this PR)
node2419.golett.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/e821199826f2bfdfe4f3023a49c9060f for a full test report.

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boegel commented Sep 14, 2019

@vanzod Does this have fixes for #7899 ?

@verdurin Should that block this PR?

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boegel commented Sep 14, 2019

Test report by @boegel
SUCCESS
Build succeeded for 9 out of 9 (5 easyconfigs in this PR)
node2128.delcatty.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/09b6be0b31b1db8dd3aaaeb3b2757200 for a full test report.

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verdurin commented Sep 15, 2019

@boegel It would seem a shame not to fix the problem when we have the opportunity.

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boegel commented Sep 16, 2019

@verdurin It doesn't seem like an easy fix though... Let's see what @vanzod thinks, since he has spent quite a bit of time with FSL recently.

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vanzod commented Sep 17, 2019

@verdurin No, it does not. As Maxime pointed out in the issue, for some of those tools FSL relies on a local installation of Miniconda and the creation of a virtual environment. It is pretty messy in my opinion and I would have needed more time than I actually have to figure out a potential way around it.
The main changes here are the addition of few more external dependencies and the setting of some environment variables in the module. This mimics what the required sourcing of fsl.sh sets.

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verdurin commented Sep 17, 2019

@vanzod Certainly I wasn't doing the work myself, and agree it's very messy. I keep meaning to contact the developers, who are pretty close to me geographically. Anyway, happy for this to be merged. Perhaps worth adding a comment in the easyconfig about the fslpython situation?

@boegel boegel modified the milestones: 4.x, 4.0.0 Sep 17, 2019
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boegel commented Sep 17, 2019

Going in, thanks @vanzod!

@boegel boegel merged commit 94a2c38 into easybuilders:develop Sep 17, 2019
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boegel commented Sep 17, 2019

Test report by @boegel
FAILED
Build succeeded for 4 out of 5 (5 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/be9a8c0d73cb33f52ed28e44a0a2d98f for a full test report.

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