{bio}[foss/2022b] HOMER v4.11.1, IMAGE v1.1, Kent_tools v461, weblogo v2.8.2 by VictorGoitea · Pull Request #20800 · easybuilders/easybuild-easyconfigs

VictorGoitea · 2024-06-12T07:46:28Z

No description provided.

change tmp directory outside of the installation directory

Co-authored-by: Sam Moors <[email protected]>

VictorGoitea · 2024-06-19T14:19:38Z

Thanks @smoors for the thorough review. I incorporated all the helpful suggestions.

smoors

a few more comments, we're almost there :)

smoors · 2024-06-20T16:18:03Z

@boegelbot: please test @ generoso

boegelbot · 2024-06-20T16:20:05Z

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

PR test command 'EB_PR=20800 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20800 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13786

Test results coming soon (I hope)...

Details

- notification for comment with ID 2181079131 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 · 2024-06-20T16:28:28Z

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 6 (6 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/3a47e8656cec42422386796cbd817bab for a full test report.

smoors · 2024-06-20T17:14:03Z

HOMER source download failed:

== 2024-06-20 16:28:15,844 filetools.py:837 WARNING IOError occurred while trying to download https://homer.ucsd.edu/homer/data/software/homer.v4.11.1.zip to /project/boegelbot/sources/h/HOMER/homer.v4.11.1.zip: <urlopen error [Errno 113] No route to host>

downloading from http seems to work though

smoors · 2024-06-21T12:23:27Z

@boegelbot: please test @ generoso

boegelbot · 2024-06-21T12:25:09Z

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

PR test command 'EB_PR=20800 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20800 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13795

Test results coming soon (I hope)...

Details

- notification for comment with ID 2182651295 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 · 2024-06-21T14:03:00Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 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/1bd7243863491dc297e3d26223db8bd8 for a full test report.

smoors · 2024-06-21T14:08:12Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-21T14:10:08Z

@smoors: 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=20800 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20800 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4444

Test results coming soon (I hope)...

Details

- notification for comment with ID 2182827681 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 · 2024-06-21T15:57:52Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/f7459c8491db2ce6eb46f1c71d3dc609 for a full test report.

smoors

lgtm

smoors · 2024-06-21T17:19:39Z

Going in, thanks @VictorGoitea!

VictorGoitea · 2024-06-24T07:39:58Z

Thanks for all the help!

VictorGoitea and others added 12 commits June 12, 2024 09:21

Added IMAGE-1.1-foss-2022b.eb easyconfig

e697b36

Update IMAGE-1.1-foss-2022b.eb

8c1ff78

Create HOMER-4.11.1-foss-2022.eb

d02ce89

Rename HOMER-4.11.1-foss-2022.eb to HOMER-4.11.1-foss-2022b.eb

c009d02

Create weblogo-2.8.2-foss-2022b.eb

4b3a54e

Update weblogo-2.8.2-foss-2022b.eb

ad85aa5

Create Kent_tools-641-GCC-12.2.0.eb

e56fe4d

Update Kent_tools-641-GCC-12.2.0.eb

b4fdec6

Fix HOMER name in IMAGE-1.1-foss-2022b.eb

9d60cb6

Fix invalid escape sequence in IMAGE-1.1-foss-2022b.eb

9e39eef

Rename Kent_tools-641-GCC-12.2.0.eb to Kent_tools-461-GCC-12.2.0.eb

6446743

Shorten long lines IMAGE-1.1-foss-2022b.eb

2e5f601

smoors changed the title ~~{bio} [foss/2022b] IMAGE 1.1~~ {bio}[foss/2022b] HOMER v4.11.1, IMAGE v1.1, Kent_tools v461, weblogo v2.8.2 Jun 12, 2024

smoors reviewed Jun 14, 2024

View reviewed changes

VictorGoitea and others added 6 commits June 19, 2024 15:30

Update HOMER-4.11.1-foss-2022b.eb

75b7824

Create libidn2-2.3.4-GCCcore-12.2.0.eb

1fb3c7e

Create wget-1.21.4-GCCcore-12.2.0.eb

c9e3f06

Update IMAGE-1.1-foss-2022b.eb

3516484

change tmp directory outside of the installation directory

Update easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb

a32d5d9

Co-authored-by: Sam Moors <[email protected]>

Update weblogo-2.8.2-foss-2022b.eb sanity_check_commands

118c2bd

Update IMAGE-1.1-foss-2022b.eb

ad94896

smoors added new update labels Jun 19, 2024

smoors reviewed Jun 19, 2024

View reviewed changes

Comment thread easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb Outdated

Comment thread easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb

Comment thread easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb

VictorGoitea added 2 commits June 20, 2024 10:12

add extract_sources = True to HOMER-4.11.1-foss-2022b.eb

abaa440

add fix_perl_shebang_for and rm mkdir /tmp in IMAGE-1.1-foss-2022b.eb

f135cf0

change back source to http HOMER-4.11.1-foss-2022b.eb

caa4df3

smoors added this to the release after 4.9.2 milestone Jun 21, 2024

smoors approved these changes Jun 21, 2024

View reviewed changes

smoors merged commit 2e2a89b into easybuilders:develop Jun 21, 2024

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VictorGoitea commented Jun 12, 2024

Uh oh!

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VictorGoitea commented Jun 19, 2024

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smoors commented Jun 20, 2024

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boegelbot commented Jun 20, 2024

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smoors commented Jun 20, 2024

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smoors commented Jun 21, 2024

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boegelbot commented Jun 21, 2024

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smoors commented Jun 21, 2024

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smoors commented Jun 21, 2024

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VictorGoitea commented Jun 24, 2024

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