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add training materials from NE BRR 2023 docker training #903

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d5216b4
started drafting training README.md
kapsakcj May 8, 2023
ed020e5
update training readme.md
kapsakcj May 8, 2023
75f372e
update training README.md
kapsakcj May 8, 2023
7ab4d46
update training README.md
kapsakcj May 8, 2023
8a1f066
update gitpod yml
kapsakcj May 8, 2023
5b14ee3
update training README.md
kapsakcj May 8, 2023
53c4649
update training README.md
kapsakcj May 8, 2023
7233c33
update training README.md to new kleborate docker image
kapsakcj May 9, 2023
7004c22
clarify how to stop gitpod env
kapsakcj May 11, 2023
4eaa469
rearrange headers
kapsakcj May 11, 2023
eb78ed1
update training readme
kapsakcj May 11, 2023
947bac8
Merge branch 'StaPH-B:master' into master
kapsakcj May 23, 2023
21604a4
added TOC to training doc
kapsakcj May 24, 2023
e4d2999
added Week 2 exercises
kapsakcj May 25, 2023
b256eeb
update TOC
kapsakcj May 25, 2023
117ebec
added line break for readability
kapsakcj May 25, 2023
79acb4d
update training README.md
kapsakcj May 31, 2023
6137487
update training readme.md. week 3 exercise
kapsakcj Jun 1, 2023
cdf8082
added TOC for week 3 exercises
kapsakcj Jun 5, 2023
e026e1e
Merge branch 'StaPH-B:master' into master
kapsakcj Jun 14, 2023
3b55510
add PDFs for slides from training
kapsakcj Jun 14, 2023
421fdaf
added PDF of week 3 exercise
kapsakcj Jun 14, 2023
280cd9e
Create CODEOWNERS
AndrewLangvt Sep 16, 2024
45a4572
Delete .github/CODEOWNERS
AndrewLangvt Sep 16, 2024
95251d9
Merge pull request #1 from StaPH-B/master
kapsakcj Sep 16, 2024
d9dcfc5
Added "Training" section to main readme with relative link to trainin…
kapsakcj Sep 16, 2024
97319f3
added info and link to APHL website for intermediate docker bioinform…
kapsakcj Sep 17, 2024
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2 changes: 1 addition & 1 deletion .gitpod.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ tasks:
pip install graphviz
. /opt/conda/etc/profile.d/conda.sh
conda activate base
git checkout main
git checkout master
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -90,6 +90,10 @@ singularity exec --bind $(pwd)/fastq:/data staphb-bbtools-38.96.simg bbduk.sh in

Further documentation can be found at [docs.sylabs.io](https://docs.sylabs.io/guides/3.1/user-guide/cli.html)

## Training

- Training materials (slides & exercises) from the North East Bioinformatics Regional Resource 2023 workshop **Docker for Public Health Bioinformatics** can be located here, within [`training/NE-BRR-docker-for-PH-bioinformatics-May2023/`](training/NE-BRR-docker-for-PH-bioinformatics-May2023/)

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## Logs

In November 2020, Docker began to implement pull rate limits for images hosted on dockerhub. This limits the number of `docker pull`'s per time period (e.g. anonymous users allowed 100 pulls per six hours). We applied and were approved for Docker's "Open Source Program," which should have removed the pull rate limits for all `staphb` docker images! 🎉 🥳 If you encounter an error such as `ERROR: toomanyrequests: Too Many Requests.` or `You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limits.` , please let us know by [submitting an issue.](https://github.com/StaPH-B/docker-builds/issues)
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