switch bamtofastq to Cargo easyblock by Micket · Pull Request #17595 · easybuilders/easybuild-easyconfigs

Micket · 2023-03-22T17:01:29Z

(created using eb --new-pr)

Requires:

new cargo easyblock new generic easyblock for installing Rust crates with cargo: Cargo and CargoPythonPackage easybuild-easyblocks#2902
enhance Cargo constructor to avoid processing list of crates multiple times into sources easybuild-easyblocks#2934

but apparently, it needs more work first, it's not finding the vendored sources for some reason

Micket · 2023-03-22T17:04:00Z

@boegel looks like this needs more work, it's not finding vendored sources for some reason

Micket · 2023-03-22T19:04:21Z

So, i cheated a bit, renamed the github source tarball so that my checksum json thing in cargo easyblock will work. Not very robust strategy though.

boegel · 2023-03-27T10:05:20Z

@Micket Let's discuss this in the EasyBuild conf call this week?

Micket · 2023-04-08T15:16:10Z

@boegelbot please test @ generoso
EB_ARGS="--include-easyblocks-from-pr 2902"

Micket · 2023-04-08T15:18:50Z

Test report by @Micket
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
vera-c1 - Linux Rocky Linux 8.6, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/Micket/b728ecd040d396c3e6e46647493539f3 for a full test report.

boegelbot · 2023-04-08T15:20:09Z

@Micket: Request for testing this PR well received on login1

PR test command 'EB_PR=17595 EB_ARGS="--include-easyblocks-from-pr 2902" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17595 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10607

Test results coming soon (I hope)...

Details

- notification for comment with ID 1500912080 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 · 2023-04-08T15:23:59Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/c55ee2642fc8ec909ff82aeaabd44012 for a full test report.

Micket · 2023-04-13T18:19:25Z

Test report by @Micket
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
vera-c1 - Linux Rocky Linux 8.6, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/Micket/30e7f5c42de5aa9cb0fb7b01f863c95f for a full test report.

Micket · 2023-05-10T16:37:11Z

Test report by @Micket
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
vera-c1 - Linux Rocky Linux 8.7, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/Micket/c610e966822dc14c8a29486c4911f048 for a full test report.

boegel · 2023-05-23T16:19:39Z

@boegelbot please test @ jsc-zen2
EB_ARGS="--include-easyblocks-from-pr 2902"

boegelbot · 2023-05-23T16:22:10Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17595 EB_ARGS="--include-easyblocks-from-pr 2902" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17595 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2658

Test results coming soon (I hope)...

Details

- notification for comment with ID 1559770393 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 · 2023-05-23T17:21:54Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
FAILED
Build succeeded for 1 out of 2 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/265e84b1fd062a3a0baa106489f1e067 for a full test report.

boegel · 2023-05-23T20:52:16Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3165.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/6e80af569ada1983b47564f8f793121e for a full test report.

boegel · 2023-05-24T05:39:12Z

@boegelbot please test @ generoso
EB_ARGS="--include-easyblocks-from-pr 2902"

boegelbot · 2023-05-24T05:40:08Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=17595 EB_ARGS="--include-easyblocks-from-pr 2902" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17595 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10852

Test results coming soon (I hope)...

Details

- notification for comment with ID 1560485095 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 · 2023-05-24T05:44:02Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2902
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/468cdacc550cba8e0b4d595065fc66da for a full test report.

boegel · 2023-05-24T14:58:30Z

@boegelbot please test @ generoso
EB_ARGS="--include-easyblocks-from-pr 2934"

boegelbot · 2023-05-24T15:00:25Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=17595 EB_ARGS="--include-easyblocks-from-pr 2934" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17595 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10868

Test results coming soon (I hope)...

Details

- notification for comment with ID 1561321067 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 · 2023-05-24T15:03:59Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2934
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns5 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/85fa701e35e949dc829c71b9614e75de for a full test report.

boegel

lgtm

boegel · 2023-05-24T16:33:31Z

Going in, thanks @Micket!

Switch bamtofastq to cargo easyblock

7d38ff5

Micket added this to the next release (4.7.2?) milestone Mar 22, 2023

boegel added the enhancement label Mar 27, 2023

Workaround cargo limitations, add missing vendored sources

d9c502a

boegel changed the title ~~Switch bamtofastq to cargo easyblock~~ switch bamtofastq to Cargo easyblock Apr 12, 2023

Add checksums for all crates

10412a6

boegel mentioned this pull request May 24, 2023

new generic easyblock for installing Rust crates with cargo: Cargo and CargoPythonPackage easybuilders/easybuild-easyblocks#2902

Merged

easybuilders deleted a comment from boegelbot May 24, 2023

boegel force-pushed the 20230322180124_new_pr_bamtofastq140 branch from af6542c to 10412a6 Compare May 24, 2023 15:58

easybuilders deleted a comment from boegelbot May 24, 2023

boegel approved these changes May 24, 2023

View reviewed changes

boegel mentioned this pull request May 24, 2023

figure out how to control version of Rust packages that are installed as dependency #15763

Closed

boegel merged commit 841d3d5 into easybuilders:develop May 24, 2023

boegel mentioned this pull request Jun 21, 2023

{bio}[GCCcore/8.3.0] Varlociraptor v1.5.0 #9491

Closed

Micket deleted the 20230322180124_new_pr_bamtofastq140 branch October 11, 2023 21:44

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Micket commented Mar 22, 2023 •

edited by boegel

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