Add sars anvil tutorial #4250

nakucher · 2023-07-02T21:58:42Z

Excited to contribute the GDSCN SARS with Galaxy in AnVIL (https://jhudatascience.org/GDSCN_Book_SARS_Galaxy_on_AnVIL/index.html) tutorial to the GTN! This is my first tutorial so please feel free to help me fix anything that needs fixing.

hexylena

Hey @nakucher, welcome to the GTN! Great to see this. I've made some comments, and there are some more comments from the review bot that you'll find in the 'files' tab.

topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.md

…utorial.md Co-authored-by: Helena <[email protected]>

nakucher · 2023-07-04T21:41:19Z

@hexylena I am getting this error in the Accessibility Linting regarding the time_estimation tutorial.md metadata (this also happened as I tested building the site with gitpod). I've tried copy/pasting directly from other tutorials to match the formatting with no luck. Any ideas?

Liquid Exception: undefined method []' for nil:NilClass in /home/runner/work/training-material/training-material/_layouts/tutorial_hands_on.html bundler: failed to load command: jekyll (/home/runner/work/training-material/training-material/vendor/bundle/ruby/3.0.0/bin/jekyll) /home/runner/work/training-material/training-material/_plugins/jekyll-duration.rb:34:in duration_to_human': undefined method `[]' for nil:NilClass (NoMethodError)

nakucher · 2023-07-10T06:52:28Z

@hexylena all checks passed! would it be possible to merge?

hexylena

Some comments :)

hexylena · 2023-07-10T06:54:20Z

CONTRIBUTORS.yaml

+    avatar: https://www.genome.gov/themes/custom/nhgri/assets/global/NHGRI-logo.svg
+    url: https://www.genome.gov/
+    funder: true
+    funding_id: 75N92022P00232


Looking for the funding IDs I find links like
https://reporter.nih.gov/search/15E8C00F4784C1D77598B8961CAA4A01A2FFCEB861BF/projects?shared=true&legacy=1&sl=15E8C00F4784C1D77598B8961CAA4A01A2FFCEB861BF

but that seems to be broken, hmm. Normally we link out to those pages but here I'm not sure it's possible which is unfortunate

Hmm yes it looks like RePORTER has been down for a little while :(

hexylena · 2023-07-10T06:58:12Z

topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.md

+- Become familiar with reference genomes and alignments
+- Explore the file structure of genomic data and quality scoring
+
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=MEZP_AzlLyg" target="https://youtu.be/MEZP_AzlLyg"><img src="http://img.youtube.com/vi/MEZP_AzlLyg/0.jpg" alt="Video thumbnail image for the Alignments background video." width="240" height="180" border="10" /></a>


Maybe someday, if y'all keep working on this, it could be interesting to integrate these slides directly into the GTN. Then you could take advantage of our automated videos to keep videos up to date. e.g. https://training.galaxyproject.org/training-material/videos/

Totally agree! I'd love to do that in the near future.

topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.md

hexylena · 2023-07-10T07:02:23Z

topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.md

+>
+>Using this formula, we can calculate that a quality score of 40 means only 0.00010 probability of an error!
+>
+> Learn more from the [Quality Control Tutorial FAQs](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/faqs/).


This should have triggered an alert but somehow it avoided it. Need to investigate that at some later date.

topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.md

…utorial.md Co-authored-by: Helena <[email protected]>

hexylena · 2023-07-10T07:16:56Z

Ok good it's failing now 😈 (sorry, but it should've been detecting the 'bad' links!)

nakucher added 8 commits July 2, 2023 13:45

Publish changes

853ce2e

add-sars-in-anvil-screenshots

935a145

add-links-for-images

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update-contributors.yaml

8b8b50c

update-contributors.yaml

77db020

add-time-estimation

b4cd870

add-billing-info

f5ab929

add-conclusion

61e378e

github-actions bot added template-and-tools sequence-analysis labels Jul 2, 2023

nakucher marked this pull request as ready for review July 2, 2023 22:00

nakucher requested a review from a team as a code owner July 2, 2023 22:00

hexylena reviewed Jul 4, 2023

View reviewed changes

nakucher and others added 7 commits July 4, 2023 15:49

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

0f4c153

…utorial.md Co-authored-by: Helena <[email protected]>

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

624f163

…utorial.md Co-authored-by: Helena <[email protected]>

add-funder-update-toc

21dbcf4

add-qc-faqs

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fix-funding-key

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test-<figure>-for-yt-video-lint

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fix-video-target

4b04e8d

nakucher and others added 5 commits July 4, 2023 22:14

add-zenodo-and-minor-fixes

ad69e96

Merge branch 'galaxyproject:main' into add-sars-anvil-tutorial

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Merge branch 'main' into add-sars-anvil-tutorial

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add-tag

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fix-image-links

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hexylena reviewed Jul 10, 2023

View reviewed changes

nakucher and others added 2 commits July 10, 2023 17:09

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

8d80c23

…utorial.md Co-authored-by: Helena <[email protected]>

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

851b0c2

…utorial.md Co-authored-by: Helena <[email protected]>

nakucher and others added 9 commits July 10, 2023 17:09

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

ccc4b22

…utorial.md Co-authored-by: Helena <[email protected]>

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

8ac91d1

…utorial.md Co-authored-by: Helena <[email protected]>

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

834151f

…utorial.md Co-authored-by: Helena <[email protected]>

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

c171a91

…utorial.md Co-authored-by: Helena <[email protected]>

Update topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/t…

35a7b5d

…utorial.md Co-authored-by: Helena <[email protected]>

Detect both flavours of bad tool links

bebaf80

fix gtn link detection

14f6f74

Extract quality score into its own FAQ

96a7ccc

Use new FAQ

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hexylena requested review from bebatut and shiltemann as code owners July 10, 2023 07:14

nakucher and others added 5 commits July 10, 2023 07:36

fix-tool-link

e8479e1

fix qc linting complaints

cd20bd4

missed one

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ensure it does not crash if provided EN

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fix-fastqc-tool-id

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hexylena approved these changes Jul 10, 2023

View reviewed changes

hexylena merged commit 5df6976 into galaxyproject:main Jul 10, 2023
2 of 3 checks passed

nakucher deleted the add-sars-anvil-tutorial branch July 10, 2023 21:04

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Add sars anvil tutorial #4250

Add sars anvil tutorial #4250

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hexylena commented Jul 10, 2023

Add sars anvil tutorial #4250

Add sars anvil tutorial #4250

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