{bio}[foss/2020a] PIPITS v2.7 (+ ITSx, and version bumps for RDP-Classifier and VSEARCH) by bedroge · Pull Request #10558 · easybuilders/easybuild-easyconfigs

bedroge · 2020-05-01T07:54:50Z

(created using eb --new-pr)

bedroge · 2020-05-01T09:37:43Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
build.hpc.rug.nl - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz, Python 2.7.5
See https://gist.github.com/3e189708ea5263193ab5c0807e08d469 for a full test report.

boegel · 2020-05-16T07:44:17Z

conda is an easy escape here in the short term, but this is likely going to break in the not so distant future, since there's very little version restrictions on the dependencies.

I'm not sure how much of a mess this would be, but maybe trying a PythonBundle is worth a shot?

The documentation is rather poor, but the dependencies are listed in https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml.

bedroge · 2020-05-20T15:16:11Z

I went for the easy solution due to a lack of time ;-)
Maybe I'll have another look at this when I have some more time.

bedroge · 2020-10-20T09:10:52Z

Test report by @bedroge
SUCCESS
Build succeeded for 7 out of 7 (4 easyconfigs in this PR)
build.hpc.rug.nl - Linux centos linux 7.4.1708, x86_64, Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz, Python 2.7.5
See https://gist.github.com/3db6eaec97221c5320c26b95cc422fa3 for a full test report.

bedroge · 2020-10-20T09:39:25Z

Test report by @bedroge
SUCCESS
Build succeeded for 8 out of 8 (5 easyconfigs in this PR)
build.hpc.rug.nl - Linux centos linux 7.4.1708, x86_64, Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz, Python 2.7.5
See https://gist.github.com/8c3020e4abff2e7ffa0b83953ba52565 for a full test report.

bedroge · 2020-10-20T11:27:57Z

@boegel I changed this from a Conda installation to an installation from source. It also includes version bumps for some existing easyconfigs (HMMER, RDP-Classifier, VSEARCH) and a new one (ITSx).

bedroge · 2020-10-20T11:45:58Z

Test report by @bedroge
SUCCESS
Build succeeded for 8 out of 8 (5 easyconfigs in this PR)
build.hpc.rug.nl - Linux centos linux 7.4.1708, x86_64, Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz, Python 2.7.5
See https://gist.github.com/73ef587eacd52f94ca353956dfb1d42f for a full test report.

…44_new_pr_PIPITS27

boegel · 2021-02-17T14:53:57Z

@boegelbot please test @ generoso

boegelbot · 2021-02-17T14:55:23Z

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

PR test command 'EB_PR=10558 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_10558 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13856

Test results coming soon (I hope)...

Details

- notification for comment with ID 780610322 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 · 2021-02-17T14:58:36Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
generoso-x-3 - 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/eeba651d80bee20ec87b0ae4d804dfb5 for a full test report.

boegel · 2021-02-17T16:32:06Z

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (4 easyconfigs in total)
node3544.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/acdd4cccd71a6898fa5c8b5d0cbf2783 for a full test report.

boegel · 2021-02-17T16:33:41Z

@boegelbot please test @ generoso

boegel · 2021-02-17T16:35:03Z

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (4 easyconfigs in total)
node3108.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/9851bf7bedf69d77782e43008297dca2 for a full test report.

boegelbot · 2021-02-17T16:35:07Z

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

PR test command 'EB_PR=10558 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_10558 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13864

Test results coming soon (I hope)...

Details

- notification for comment with ID 780682691 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 · 2021-02-17T16:36:02Z

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (4 easyconfigs in total)
node2614.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/998f6c4ffb646a3fa785ec571d6af4eb for a full test report.

boegelbot · 2021-02-17T16:37:57Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/7d6ab7bb2d75b056b972ae39683ec775 for a full test report.

boegel · 2021-02-17T16:40:48Z

Going in, thanks @bedroge!

bedroge added 2 commits May 1, 2020 09:54

adding easyconfigs: PIPITS-2.7.eb

c95958d

Removed some trailing whitespaces

9e7131f

boegel added the new label May 16, 2020

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

replace conda installtion by source installation

2a98c0a

bedroge added 2 commits October 20, 2020 11:12

added checksums

4da4d41

added new version of RDP-Classifier which uses Java 11

5eef12f

bedroge added 4 commits October 20, 2020 11:46

include pyver in versionsuffix / filename

860fa09

remove use_pip

efc0ace

set use_pip and sanity_pip_check = True

bfd671a

use https for RDP-Classifier website

1779f89

bedroge changed the title ~~{bio}[system/system] PIPITS v2.7~~ {bio}[foss/2020a] PIPITS v2.7 (+ ITSx, and version bumps for HMMER, RDP-Classifier, VSEARCH) Oct 20, 2020

bedroge added 4 commits February 17, 2021 14:45

Merge github.com:easybuilders/easybuild-easyconfigs into 202005010954…

637805a

…44_new_pr_PIPITS27

remove customized HMMER easyconfigs, use existing one

ff1edf3

rename file

6a615e1

remove binutils from build deps

f649d84

bedroge changed the title ~~{bio}[foss/2020a] PIPITS v2.7 (+ ITSx, and version bumps for HMMER, RDP-Classifier, VSEARCH)~~ {bio}[foss/2020a] PIPITS v2.7 (+ ITSx, and version bumps for RDP-Classifier and VSEARCH) Feb 17, 2021

boegel requested changes Feb 17, 2021

View reviewed changes

Comment thread easybuild/easyconfigs/i/ITSx/ITSx-1.1.2-GCCcore-9.3.0.eb

Comment thread easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb

Comment thread easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.15.0-GCC-9.3.0.eb

bedroge added 2 commits February 17, 2021 15:58

add sanity check command

c975fac

add sanity check command

9571c70

add sanity check command

066e65c

boegel approved these changes Feb 17, 2021

View reviewed changes

boegel merged commit 44980c6 into easybuilders:develop Feb 17, 2021

bedroge deleted the 20200501095444_new_pr_PIPITS27 branch February 17, 2021 16:41

boegel modified the milestones: 4.x, next release (4.3.3?) Feb 17, 2021

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bedroge commented May 1, 2020

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