{bio}[foss/2020b} pangolin v3.1.10 by sassy-crick · Pull Request #13733 · easybuilders/easybuild-easyconfigs

sassy-crick · 2021-08-13T11:39:28Z

(created using eb --new-pr)

edit: requires ~~#13708~~ (UShER), ~~#13651~~ (gofasta)

Micket · 2021-08-13T12:17:31Z

+    }),
+    ('constellations', '0.0.13', {
+        'source_urls': ['https://github.com/%(github_account)s/%name)s/archive'],
+        'sources': [{'download_filename': 'v%(version).tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],


Suggested change

'sources': [{'download_filename': 'v%(version).tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],

'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],

Thanks for finding them! I simply did not spot them. (I do need new glasses, not a joke). I have corrected them.
By the way, is there a way to avoid these repeating lines?

Converted to draft as we are waiting to have UShER merged.

By the way, is there a way to avoid these repeating lines?

You can likely put them into exts_default_options (dict that is merged with this dict) although I'm not fully sure it works with the templates, but please try.
Also use SOURCE_TAR_GZ as the filename and GITHUB_SOURCE as the source_url, see https://docs.easybuild.io/en/latest/version-specific/easyconfig_templates.html

Converted to draft as we are waiting to have UShER merged.

If that is the only thing then simply mention it in the PR description like: - [ ] Requires #13708

Flamefire · 2021-08-17T13:27:11Z

The dependencies and extensions seem a bit off. I guess you used https://github.com/cov-lineages/pangolin/blob/master/environment.yml as a reference?
Checking https://github.com/cov-lineages/pangolin/blob/504d9833f4715c26b08b30e1cd2ad859d358c721/setup.py#L14-L22 there seem to be a few Python packages missing. E.g. pandas. Can you double check those?

SethosII · 2021-08-17T13:57:39Z

@Flamefire pandas for example is included in SciPy-bundle

sassy-crick · 2021-08-17T15:58:08Z

The dependencies and extensions seem a bit off. I guess you used https://github.com/cov-lineages/pangolin/blob/master/environment.yml as a reference?
Yes, that is what I done and also added what was missing when I installed it. This is where the scikit-learn for example came from.
@SethosII has already addressed the issue with pandas I will look into the other two I noticed joblib and PuLP and see if they are really missing or being pulled in.
I noticed that for scikit-learn SciPy-bundle is a requirement so we could remove that one.

Flamefire · 2021-08-18T07:20:29Z

I noticed that for scikit-learn SciPy-bundle is a requirement so we could remove that one.

Keep it. It is better to have the direct dependencies explicit in case the others change in a later version

sassy-crick · 2021-08-22T22:32:51Z

The dependencies and extensions seem a bit off. I guess you used https://github.com/cov-lineages/pangolin/blob/master/environment.yml as a reference?
Yes, that is what I done and also added what was missing when I installed it. This is where the scikit-learn for example came from.

@SethosII has already addressed the issue with pandas. I have checked this link and compared it with what I got:

pandas                        1.1.4  (>=1.0.1)
wheel                         0.35.1 (>=0.34)
joblib                        0.17.0 (>=0.11)
pysam                         0.16.0.1 (>1.16.0)
scikit-learn                  0.23.2 (>= 0.23.1)
PuLP                          2.4 ((>=2)

So that should be ok.

I looked into getting the repeating lines in the extension list a bit more neat. I replaced the URLs with the GITHUB_SOURCE as suggested. However, the SOURCE_TAR_GZ will only work in one case as all the others are named v-name-version.tar.gz. I tried to put the checksums outside the exts_list but here the style-check failed.

sassy-crick · 2021-08-22T22:38:46Z

Additionally, to move forward, added Kent_tools so I can removed them from UShER

…his module

boegel · 2021-08-28T08:43:04Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3582.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/7821359089b03a595ecfa5f248427bae for a full test report.

boegel · 2021-08-28T08:43:09Z

@boegelbot please test @ generoso

boegelbot · 2021-08-28T08:45:09Z

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

PR test command 'EB_PR=13733 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13733 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 18231

Test results coming soon (I hope)...

Details

- notification for comment with ID 907594993 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 · 2021-08-28T08:46:50Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-6 - 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/0f1dda9fae82bc6f524dfc2608182eb0 for a full test report.

boegel · 2021-08-28T08:53:43Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2609.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/77c558db9afc772baa7b54fce897ade2 for a full test report.

typos fixed

SethosII · 2021-08-28T09:04:37Z

@@ -0,0 +1,80 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# Based on a EC provided by Paul Jähn


Just a nitpick: my last name has an e at the end ;)

Suggested change

# Based on a EC provided by Paul Jähn

# Based on a EC provided by Paul Jähne

SethosII · 2021-08-28T09:22:20Z

+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [


I would also add pangolin -v:

Suggested change

sanity_check_commands = [

sanity_check_commands = [

'pangolin -v',

boegel

lgtm

boegel · 2021-08-28T09:31:07Z

Going in, thanks @sassy-crick!

pangolin 3.1.10 created

b9ebe6f

sassy-crick changed the title ~~pangolin 3.1.10 created~~ {BIO}[foss/2020b} pangolin 3.1.10 created Aug 13, 2021

This was referenced Aug 13, 2021

{bio}[GOMPI-2020a] UShER 0.4.1 created. #13694

Closed

{bio}[foss/2018b] pangolin 3.0.5 w/ Python 3.7.0 and dependencies #13119

Closed

{bio}[foss/2021a] pangolin v3.1.10 w/ Python 3.9.5 #13681

Closed

sassy-crick changed the title ~~{BIO}[foss/2020b} pangolin 3.1.10 created~~ {bio}[foss/2020b} pangolin 3.1.10 created Aug 13, 2021

Micket requested changes Aug 13, 2021

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Comment thread easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb Outdated

Micket previously requested changes Aug 13, 2021

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Typos corrected

29d6aab

sassy-crick marked this pull request as draft August 13, 2021 19:56

boegel added the new label Aug 14, 2021

boegel added this to the 4.x milestone Aug 14, 2021

sassy-crick mentioned this pull request Aug 17, 2021

{bio}[gompi/2020b] UShER v0.4.1 w/ Python 3.8.6 #13708

Merged

1 task

Flamefire reviewed Aug 17, 2021

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Comment thread easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb Outdated

Flamefire reviewed Aug 17, 2021

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Comment thread easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb Outdated

Some tidy up in the extension-list: replaced URLs with GITHUB_SOURCE

ae20e5d

sassy-crick changed the title ~~{bio}[foss/2020b} pangolin 3.1.10 created~~ {bio}[foss/2020b} pangolin 3.1.10 created Requires #13708 or #13694 Aug 22, 2021

Kent_tools added as removed from UShER PR 13694

4be7724

Explicitly stated in module description that faToVcf is included in t…

633e67b

…his module

sassy-crick changed the title ~~{bio}[foss/2020b} pangolin 3.1.10 created Requires #13708 or #13694~~ {bio}[foss/2020b} pangolin 3.1.10 created Aug 27, 2021

minimap2 downgraded to 2.18 to honor the one version rule

87e7639

sassy-crick marked this pull request as ready for review August 27, 2021 18:56

easybuilders deleted a comment from boegelbot Aug 28, 2021

boegel changed the title ~~{bio}[foss/2020b} pangolin 3.1.10 created~~ {bio}[foss/2020b} pangolin v3.1.10 Aug 28, 2021

boegel modified the milestones: 4.x, next release (4.4.2?) Aug 28, 2021

clean up pangolin easyconfig by leveraging exts_default_options

e271070

Flamefire approved these changes Aug 28, 2021

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SethosII suggested changes Aug 28, 2021

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boegel approved these changes Aug 28, 2021

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boegel merged commit 14e889b into easybuilders:develop Aug 28, 2021

branfosj mentioned this pull request Aug 28, 2021

correct the version, fix spelling of a name, and add an extra sanity check command in pangolin #13848

Merged

sassy-crick deleted the 20210813113839_new_pr_pangolin3110 branch August 28, 2021 15:00

	'sources': [{'download_filename': 'v%(version).tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
	'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],

	# Based on a EC provided by Paul Jähn
	# Based on a EC provided by Paul Jähne

	sanity_check_commands = [
	sanity_check_commands = [
	'pangolin -v',

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sassy-crick commented Aug 13, 2021 •

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sassy-crick commented Aug 22, 2021 •

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