{bio}[foss/2023a] phyluce v1.7.3 by pavelToman · Pull Request #19779 · easybuilders/easybuild-easyconfigs

pavelToman · 2024-02-02T10:08:29Z

(created using eb --new-pr)

…1.7.3_fix-config-paths.patch, phyluce-1.7.3_removal-Bio-Alphabet.patch

pavelToman · 2024-02-02T10:43:12Z

@boegelbot please test @ generoso

boegelbot · 2024-02-02T10:45:08Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12815

Test results coming soon (I hope)...

Details

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boegelbot · 2024-02-02T10:57:38Z

Test report by @boegelbot
FAILED
Build succeeded for 7 out of 11 (9 easyconfigs in total)
cns3 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/5c3265d66b5a19d8f8d04a03b945436f for a full test report.

pavelToman · 2024-02-02T12:13:32Z

@boegelbot please test @ generoso

boegelbot · 2024-02-02T12:15:09Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12816

Test results coming soon (I hope)...

Details

- notification for comment with ID 1923686335 processed

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-02-02T12:31:06Z

Test report by @boegelbot
FAILED
Build succeeded for 7 out of 11 (9 easyconfigs in total)
cns2 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/1d26cf7e7d46a8b1ba43dcaf08b48281 for a full test report.

pavelToman · 2024-02-02T13:22:09Z

@boegelbot please test @ generoso

boegelbot · 2024-02-02T13:25:08Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12820

Test results coming soon (I hope)...

Details

- notification for comment with ID 1923795178 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 · 2024-02-02T13:35:18Z

Test report by @boegelbot
FAILED
Build succeeded for 6 out of 10 (9 easyconfigs in total)
cns3 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/5bdac644b64b94bd908b4d38276f62b1 for a full test report.

pavelToman · 2024-02-06T10:23:16Z

@boegelbot please test @ generoso

boegelbot · 2024-02-06T10:25:09Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12837

Test results coming soon (I hope)...

Details

- notification for comment with ID 1929204423 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).

pavelToman · 2024-02-06T10:41:17Z

@boegelbot please test @ generoso

boegelbot · 2024-02-06T10:45:09Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12838

Test results coming soon (I hope)...

Details

- notification for comment with ID 1929236533 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 · 2024-02-06T10:56:04Z

Test report by @boegelbot
FAILED
Build succeeded for 6 out of 10 (9 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/6fbd581d95b66a2d30ae006f2eebd939 for a full test report.

pavelToman · 2024-02-06T11:32:57Z

@boegelbot please test @ generoso

boegelbot · 2024-02-06T11:35:09Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12839

Test results coming soon (I hope)...

Details

- notification for comment with ID 1929329943 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 · 2024-02-06T11:53:26Z

Test report by @boegelbot
FAILED
Build succeeded for 8 out of 10 (9 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ad794ab4bd5fae5762d45c6b88c0f65f for a full test report.

pavelToman · 2024-02-07T11:37:27Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-02-07T11:40:08Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3571

Test results coming soon (I hope)...

Details

- notification for comment with ID 1931859365 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 · 2024-02-07T11:55:49Z

Test report by @boegelbot
SUCCESS
Build succeeded for 19 out of 19 (9 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/93c4f9e3ed4f06da9f54058bbecfdc29 for a full test report.

boegel

fix versionsuffix for Pilon

boegel · 2024-02-07T19:30:39Z

Test report by @boegel
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
node3120.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/eed8d5f60988771f57452ba85b63a34c for a full test report.

boegel · 2024-02-07T19:30:59Z

@boegelbot please test @ generoso

boegelbot · 2024-02-07T19:35:11Z

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

PR test command 'EB_PR=19779 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19779 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12850

Test results coming soon (I hope)...

Details

- notification for comment with ID 1932729575 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 · 2024-02-07T19:55:59Z

Test report by @boegelbot
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b12fb9b970f2ff3e0a3f2cb9b901c2e0 for a full test report.

boegel · 2024-02-07T22:05:40Z

Going in, thanks @pavelToman!

pavelToman added 5 commits February 2, 2024 11:08

adding easyconfigs: phyluce-1.7.3-foss-2023a.eb and patches: phyluce-…

d246f59

…1.7.3_fix-config-paths.patch, phyluce-1.7.3_removal-Bio-Alphabet.patch

add deps 1

cd9ecd3

add deps 2

3aab293

add deps 3

b57d3ea

fix format

ffc5047

pavelToman mentioned this pull request Feb 2, 2024

phyluce vscentrum/vsc-software-stack#271

Closed

pavelToman added 3 commits February 2, 2024 12:07

fix snakemake version

b367f72

add patches descriptions

e6f34a6

fix patches cheksums

71f8671

changed to PythonPavkage easyblock

1dfbf8e

pavelToman added 2 commits February 2, 2024 14:50

fix indents

018bcd7

add download_dep_fail

c309998

fix btllib checksum

81c9a54

fix too long line

42140df

remove download_dep_fail

4fb6728

easybuilders deleted a comment from boegelbot Feb 7, 2024

boegel added new update labels Feb 7, 2024

boegel added this to the 4.x milestone Feb 7, 2024

boegel added 5 commits February 7, 2024 19:41

stick to GCC toolchain for LASTZ

e59c85c

add pilon wrapper script to existing Pilon easyconfig

f6e5f3f

add sanity check command for trimAl

c43ff54

remove explicit OpenMPI dependency in ABySS easyconfig

ebc0b9a

add missing authorship in patches for phyluce

73802aa

boegel requested changes Feb 7, 2024

View reviewed changes

Comment thread easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb Outdated

fix versionsuffix for Pilon

c56968a

boegel approved these changes Feb 7, 2024

View reviewed changes

boegel merged commit 59c3d3c into easybuilders:develop Feb 7, 2024

boegel modified the milestones: 4.x, 4.9.1 Apr 4, 2024

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pavelToman commented Feb 2, 2024

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