{bio}[system/system] fgbio v1.3.0 by zarybnicky · Pull Request #11519 · easybuilders/easybuild-easyconfigs

zarybnicky · 2020-10-16T13:59:42Z

(created using eb --new-pr)

boegel · 2020-10-16T14:52:17Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3402.kirlia.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/b26df0d93184daba0a838168bff3a5d7 for a full test report.

boegel · 2020-10-18T09:59:58Z

@boegelbot please test @ generoso

boegelbot · 2020-10-18T10:00:16Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11519 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11519 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8162

Test results coming soon (I hope)...

Details

- notification for comment with ID 711144555 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2020-10-18T10:02:32Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
generoso-x-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/cabc43c84d84ebdd0454f7f399e56b6e for a full test report.

zarybnicky · 2020-10-18T11:17:44Z

@boegel Is Host repo1.maven.org not found. url=https://repo1.maven.org/maven2/org/scala-sbt/sbt/1.2.8/sbt-1.2.8.pom from the logs doesn't seem like a build error I can fix - is the connectivity on generoso-x-2 good?

boegel · 2020-10-19T08:20:12Z

@zarybnicky We don't manage generoso, but it should have good connectivity to the outside world. I'll check again from a different system.

boegel · 2020-10-19T08:20:41Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node2427.golett.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (haswell), Python 2.7.5
See https://gist.github.com/781b86bcee36290166567ca52923d499 for a full test report.

boegel · 2020-10-19T08:26:08Z

@zarybnicky $HOME/.sbt is purposely set to read-only to ensure no installation tries to use it, please redefine $HOME during the installation to make it use $TMPDIR instead?

$ ls -ld /user/gent/400/vsc40023/.sbt/
dr-------- 2 vsc40023 vsc40023 4096 Nov 20  2017 /user/gent/400/vsc40023/.sbt/

zarybnicky · 2020-10-19T20:37:32Z

That's what I blindly tried, setting HOME=$TMPDIR, but it seems this isn't it. I'll look into sbt options...

zarybnicky · 2020-10-20T15:17:16Z

-sbt-dir seems to work better than just HOME=$TMPDIR, for future reference.

boegel · 2020-10-20T17:52:17Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node2709.swalot.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 2.7.5
See https://gist.github.com/1bdda0b3525bdfd770e2b409bcd0be76 for a full test report.

boegel · 2020-10-20T17:53:17Z

@zarybnicky similar issue now with $HOME/.ivy2...

verdurin · 2020-11-02T18:25:57Z

@zarybnicky any thoughts on the comment from @boegel ?

boegel · 2020-11-17T07:59:27Z

@boegelbot please test @ generoso

boegelbot · 2020-11-17T08:00:23Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11519 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11519 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9776

Test results coming soon (I hope)...

Details

- notification for comment with ID 728754942 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegel · 2020-11-17T08:01:58Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3166.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/98e238f854d2a6a4f24c932b89365012 for a full test report.

boegelbot · 2020-11-17T08:04:08Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/2c9503e7cc86b22f4f9d06641bbe55cb for a full test report.

boegel · 2020-11-17T08:31:23Z

@boegelbot please test @ generoso

boegel · 2020-11-17T08:34:58Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
node2632.swalot.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 2.7.5
See https://gist.github.com/8d5497e156a6faf2ab30bf732b631820 for a full test report.

boegelbot · 2020-11-17T08:35:08Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11519 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11519 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9777

Test results coming soon (I hope)...

Details

- notification for comment with ID 728772447 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2020-11-17T08:38:20Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/484bba0d97039349d906d643729fbb15 for a full test report.

boegel · 2020-11-17T09:06:59Z

@boegelbot please test @ generoso

boegel · 2020-11-17T09:09:55Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3407.kirlia.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/2f1b5ab82a806fe76986f93ebf6b8a3b for a full test report.

boegel · 2020-11-17T09:10:01Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3166.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/8db26c189c7b2a4e10a36a604403c5c8 for a full test report.

boegelbot · 2020-11-17T09:10:18Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11519 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11519 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9779

Test results coming soon (I hope)...

Details

- notification for comment with ID 728791227 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegel · 2020-11-17T09:12:40Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2632.swalot.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 2.7.5
See https://gist.github.com/8e3827dd25758169aa082aa1563e3868 for a full test report.

boegelbot · 2020-11-17T09:13:28Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/37067a9679b73b6f8f1620e5d062a2de for a full test report.

boegel · 2020-11-17T10:32:08Z

Going in, thanks @zarybnicky!

adding easyconfigs: fgbio-1.3.0.eb

20e95dc

boegel requested changes Oct 16, 2020

View reviewed changes

Comment thread easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb Outdated

Comment thread easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb Outdated

boegel added the new label Oct 16, 2020

boegel added this to the 4.x milestone Oct 16, 2020

fgbio: fix .sbt/ build location

dfe6d17

fgbio: fix .sbt/ build location

d8c04ca

avoid using $HOME/.ivy2 during installation of fgbio

48dbbb3

resolve path to 'java' in fgbio wrapper script

9ede1da

add Java runtime dependency to fgbio easyconfig

bbf368b

use %(javaver)s template

a601f7c

boegel approved these changes Nov 17, 2020

View reviewed changes

boegel merged commit 5b0609d into easybuilders:develop Nov 17, 2020

zarybnicky deleted the 20201016155935_new_pr_fgbio130 branch November 18, 2020 09:33

migueldiascosta modified the milestones: 4.x, 4.3.2 (next release) Dec 9, 2020

Conversation

zarybnicky commented Oct 16, 2020

Uh oh!

Uh oh!

Uh oh!

boegel commented Oct 16, 2020

Uh oh!

boegel commented Oct 18, 2020

Uh oh!

boegelbot commented Oct 18, 2020

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boegelbot commented Oct 18, 2020

Uh oh!

zarybnicky commented Oct 18, 2020

Uh oh!

boegel commented Oct 19, 2020

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zarybnicky commented Oct 19, 2020

Uh oh!

zarybnicky commented Oct 20, 2020

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boegel commented Oct 20, 2020

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boegel commented Oct 20, 2020

Uh oh!

verdurin commented Nov 2, 2020

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boegel commented Nov 17, 2020

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boegel commented Nov 17, 2020

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boegel commented Nov 17, 2020

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boegel commented Nov 17, 2020

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boegel commented Nov 17, 2020

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boegel commented Nov 17, 2020

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boegel commented Nov 17, 2020

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