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{bio}[foss/2018a] shovill v0.9.0, KMC v3.1.0, Lighter v1.1.1, Pilon 1.22, SKESA 2.9.1 #6553

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verdurin merged 3 commits intoeasybuilders:developfrom
boegel:20180704165618_new_pr_shovill090
Sep 23, 2018
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{bio}[foss/2018a] shovill v0.9.0, KMC v3.1.0, Lighter v1.1.1, Pilon 1.22, SKESA 2.9.1 #6553
verdurin merged 3 commits intoeasybuilders:developfrom
boegel:20180704165618_new_pr_shovill090

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@boegel boegel commented Jul 4, 2018 •
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(created using eb --new-pr)
requires #6543 (BWA), #6542 (Mash), #6544 (pigz), #6545 (SPAdes), #6546 (MEGAHIT), #6547 (FLASH), #6548 (ncbi-vdb), #6549 (seqtk), #6550 (Velvet)

@boegel boegel added the new label Jul 4, 2018
@boegel boegel force-pushed the 20180704165618_new_pr_shovill090 branch from a48fc2f to 7be49e1 Compare July 4, 2018 16:20
@boegel boegel requested a review from vanzod July 4, 2018 16:25
@boegel boegel modified the milestones: next release, 3.6.2 Jul 6, 2018
@easybuilders easybuilders deleted a comment from boegelbot Aug 21, 2018
@easybuilders easybuilders deleted a comment from boegelbot Aug 21, 2018
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boegel commented Aug 21, 2018

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
node2004.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/ad9d9cb3610089ee344b579b6189de27 for a full test report.

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boegel commented Aug 21, 2018

Test report by @boegel
SUCCESS
Build succeeded for 19 out of 19 (5 easyconfigs in this PR)
node2608.swalot.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/a4de979de8b53dbb9b7844bde843f9db for a full test report.

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verdurin commented Aug 21, 2018

Test report by @verdurin
FAILED
Build succeeded for 16 out of 18 (5 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.5.1804, Intel Xeon E312xx (Sandy Bridge), Python 2.7.5
See https://gist.github.com/3ab8fc25b65d2e6004cbc39d06f98a9e for a full test report.

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boegel commented Aug 22, 2018

@verdurin That build failure look quite suspicious... error: cannot find -lm

Was something (temporarily) broken on that system? Can you try again with eb --from-pr 6553 KMC-3.1.0-foss-2018a.eb?

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verdurin commented Aug 22, 2018

@boegel It is suspicious. However, it fails the same way.

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vanzod commented Sep 5, 2018

Test report by @vanzod
SUCCESS
Build succeeded for 8 out of 8 (5 easyconfigs in this PR)
cermis - Linux debian 9.4, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/ba31a431876fcba2bf0641aa799c90c4 for a full test report.

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vanzod commented Sep 5, 2018

@verdurin Any update on your issue? I would like to get this merged ASAP.

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verdurin commented Sep 5, 2018

@vanzod still seeing the same error, for which I have no explanation.

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boegel commented Sep 22, 2018

@verdurin Taking another look at this, it looks like the problem may be that you don't have glibc-static installed, since this is what fails:

$ g++ -lm -static ...  -o bin/kmc_dump ...
/home/centos/.local/easybuild/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -lc
/home/centos/.local/easybuild/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -lpthread
/home/centos/.local/easybuild/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -lm

So, if libm.a isn't there, that would explain the failure. On my system:

$ rpm -qf /usr/lib64/libm.a
glibc-static-2.17-222.el7.x86_64

@boegel boegel modified the milestones: 3.7.0, next release Sep 22, 2018
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verdurin commented Sep 23, 2018

@boegel yes, can confirm I don't have glibc-static installed, so that should go in osdependencies?

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verdurin commented Sep 23, 2018

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (5 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.5.1804, Intel Xeon E312xx (Sandy Bridge), Python 2.7.5
See https://gist.github.com/74882786968ea22f948c8f326c3c4a2d for a full test report.

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verdurin commented Sep 23, 2018

Test succeeded after installing glibc-static.

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boegel commented Sep 23, 2018

@verdurin Thanks for the confirmation, I think adding glibc-static as an OS dep reasonable for now.

A better option would be to prevent static linking hardcoded I guess, but that can be picked up on in a future PR if needed...

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boegel commented Sep 23, 2018

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
gligar01.gligar.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/bcd368e5ad7d43779bd8be9ddae8f496 for a full test report.

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boegel commented Sep 23, 2018

Test report by @boegel
SUCCESS
Build succeeded for 6 out of 6 (5 easyconfigs in this PR)
node2400.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/4fb686eed1226a9804cceb02c93059ac for a full test report.

verdurin
verdurin approved these changes Sep 23, 2018
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Looks good now.

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verdurin commented Sep 23, 2018

Going in, thanks @boegel!

@verdurin verdurin merged commit 6103a6e into easybuilders:develop Sep 23, 2018
@boegel boegel modified the milestones: next release, 3.7.0 Sep 24, 2018
@boegel boegel deleted the 20180704165618_new_pr_shovill090 branch September 24, 2018 14:07
boegel
boegel commented Dec 10, 2018
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Comment thread easybuild/easyconfigs/s/SKESA/SKESA-2.9.1-foss-2018a.eb
toolchain = {'name': 'foss', 'version': '2018a'}
toolchainopts = {'cstd': 'c++11'}

source_urls = ['https://github.com/ncbi/ngs-tools/archive/']
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Download location + version was correct in #7275

@migueldiascosta migueldiascosta mentioned this pull request Feb 14, 2019
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@verdurin verdurin verdurin approved these changes

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