{bio}[foss/2020b] artic-ncov2019 v2021.06.24 #13852

sassy-crick · 2021-08-30T13:42:53Z

(created using eb --new-pr)

sassy-crick · 2021-08-30T13:50:03Z

Flamefire

Needs some checks on the used dependencies/extensions to remove those already present in core Python
Besides that: Having trouble understanding how this was generated. For verification purposes: Why and where do those dependencies and extensions come from? Checking the homepage/repo I can't find those so it looks like a more or less random collection of stuff to me which makes it hard to verify

easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb

{bio}[GCCcore/10.2.0] LSD2 bumped to 2.2, required for artic #13852

…LE3831 {bio}[GCCcore/10.2.0] Muscle bumped to 3.8.31, required for artic #13852

…asyconfigs into 20210830134227_new_pr_artic-ncov201920210621

…or Eigen and TF need to stay as they are though (medaka)!

…asyconfigs into 20210830134227_new_pr_artic-ncov201920210621

Flamefire

I test-installed fieldbioinformatics on top of the dependency modules and seemingly the only required packages are:

clint-0.5.1
args-0.1.0
PyVCF-0.6.8
tqdm-4.62.3

The others are already provided by the Python Module (or others) and can be removed. I'd also suggest to move the above 4 above the fieldbioinformatics package as they are dependencies of it.

easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb

…e name from False to artic

Flamefire · 2021-09-21T15:12:51Z

Test report by @Flamefire
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
taurusi8017 - Linux centos linux 7.9.2009, x86_64, AMD EPYC 7352 24-Core Processor (zen2), Python 2.7.5
See https://gist.github.com/ca980ab1d50d3f976c5e7fe07dfbe9b1 for a full test report.

Flamefire · 2021-09-22T03:24:29Z

Test report by @Flamefire
SUCCESS
Build succeeded for 65 out of 65 (1 easyconfigs in total)
taurusa4 - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) CPU E5-2603 v4 @ 1.70GHz (broadwell), Python 2.7.5
See https://gist.github.com/2006bea7f42736d464bc97a2492cd2b7 for a full test report.

Flamefire · 2021-09-22T07:50:16Z

Test report by @Flamefire
FAILED
Build succeeded for 50 out of 66 (1 easyconfigs in total)
taurusml7 - Linux RHEL 7.6, POWER, 8335-GTX (power9le), Python 2.7.5
See https://gist.github.com/9e26cd755518b4d43354e2f2cce372d7 for a full test report.

easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb

SebastianAchilles · 2021-09-24T09:38:05Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2021-09-24T09:40:10Z

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

PR test command 'EB_PR=13852 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_13852 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 6978

Test results coming soon (I hope)...

- notification for comment with ID 926489920 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 · 2021-09-24T09:52:13Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/14fb2e671ea8421707458735bf8dbc71 for a full test report.

boegel · 2021-10-19T08:55:02Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3101.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/3cc9784ddf0fde39635a2d721e27a78c for a full test report.

boegel · 2021-10-19T08:56:52Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3513.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/cc73d9b5d6e2e0281dc8a2761bf48ef3 for a full test report.

boegel

lgtm

boegel · 2021-10-20T18:42:58Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3157.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/9cd84038b5784795d69f2552c8ec607b for a full test report.

boegel · 2021-10-20T20:11:07Z

Going in, thanks @sassy-crick!

artic updated to latest version and foss-2020b, WIP

e8b87aa

sassy-crick marked this pull request as draft August 30, 2021 13:48

sassy-crick mentioned this pull request Aug 30, 2021

{bio}[foss/2020b] medaka v1.4.3 w/ Python 3.8.6 #13853

Merged

4 tasks

Flamefire suggested changes Aug 31, 2021

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sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{bio}[GCCcore/10.2.0] LSD2 bumped to 2.2, required for artic easybuil…

33ec7cf

…ders#13852

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{bio}[GCCcore/10.2.0] Longshot bumped to 0.4.3, required for artic ea…

30e0a63

…sybuilders#13852

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{bio}[GCCcore/10.2.0] Muscle bumped to 3.8.31, required for artic eas…

45c1a00

…ybuilders#13852

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{bio}[GCCcore/10.2.0] Racon bumped to 1.4.21, required for artic easy…

d113969

…builders#13852

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{lang}[GCCcore/10.2.0] Rust bumped to 1.52.1, required for artic easy…

b308678

…builders#13852

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{bio}[GCCcore/10.2.0] edlib bumped to 1.3.9, required for artic easyb…

ec3af08

…uilders#13852

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Sep 15, 2021

{tools}[foss/2020b] networkx bumped to 2.6.2, required for artic easy…

2679197

…builders#13852

verdurin added a commit that referenced this pull request Sep 15, 2021

Merge pull request #13992 from sassy-crick/20210915123627_new_pr_LSD222

811d8b7

{bio}[GCCcore/10.2.0] LSD2 bumped to 2.2, required for artic #13852

Updated file to final version, corrected version or artic to 24.6.2020

fd4a584

sassy-crick changed the title ~~artic updated to latest version and foss-2020b, WIP~~ artic updated to latest version and foss-2020b Sep 16, 2021

sassy-crick changed the title ~~artic updated to latest version and foss-2020b~~ {bio}[foss/2020b] artic ncov2019-2021.06.24 Sep 16, 2021

Added missing artic_get_stats script

c40440e

SebastianAchilles added a commit that referenced this pull request Sep 20, 2021

Merge pull request #13996 from sassy-crick/20210915134014_new_pr_MUSC…

883e01a

…LE3831 {bio}[GCCcore/10.2.0] Muscle bumped to 3.8.31, required for artic #13852

Sassy added 2 commits September 20, 2021 12:14

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

c9d2def

…asyconfigs into 20210830134227_new_pr_artic-ncov201920210621

Surplus ont-fast5-api module removed

3ecd2fd

sassy-crick marked this pull request as ready for review September 20, 2021 12:19

Downgraded SAMtools and BCFtools to 1.11, minimap2 to 2.18. Version f…

dd03020

…or Eigen and TF need to stay as they are though (medaka)!

SebastianAchilles mentioned this pull request Sep 20, 2021

add exception to easyconfigs test suite for (indirect) TensorFlow 2.2.3 dependency for artic-ncov2019 #14037

Merged

Sassy added 2 commits September 20, 2021 14:42

Removed Eigen as dependency

97d1377

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

61e338c

…asyconfigs into 20210830134227_new_pr_artic-ncov201920210621

Flamefire suggested changes Sep 21, 2021

View reviewed changes

easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb Outdated Show resolved Hide resolved

Removed apparently surplus Python modules as suggested, changed modul…

c48583b

…e name from False to artic

Flamefire reviewed Sep 24, 2021

View reviewed changes

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easybuilders deleted a comment from boegelbot Sep 28, 2021

boegel changed the title ~~{bio}[foss/2020b] artic ncov2019-2021.06.24~~ {bio}[foss/2020b] artic-ncov2019 v2021.06.24 Sep 28, 2021

boegel added the update label Sep 28, 2021

boegel added this to the 4.x milestone Sep 28, 2021

use proper tqdm dependency in artic-ncov2019 easyconfig

8eae489

boegel approved these changes Oct 20, 2021

View reviewed changes

boegel modified the milestones: 4.x, 4.5.0 (next release) Oct 20, 2021

boegel merged commit 6ffa4e1 into easybuilders:develop Oct 20, 2021

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{bio}[foss/2020b] artic-ncov2019 v2021.06.24 #13852

{bio}[foss/2020b] artic-ncov2019 v2021.06.24 #13852

sassy-crick commented Aug 30, 2021

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edited by SebastianAchilles

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{bio}[foss/2020b] artic-ncov2019 v2021.06.24 #13852

{bio}[foss/2020b] artic-ncov2019 v2021.06.24 #13852

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edited by SebastianAchilles