add training materials from NE BRR 2023 docker training (#903)

* started drafting training README.md * update training readme.md * update training README.md * update training README.md * update gitpod yml * update training README.md * update training README.md * update training README.md to new kleborate docker image * clarify how to stop gitpod env * rearrange headers * update training readme * added TOC to training doc * added Week 2 exercises * update TOC * added line break for readability * update training README.md * update training readme.md. week 3 exercise * added TOC for week 3 exercises * add PDFs for slides from training * added PDF of week 3 exercise * Create CODEOWNERS * Delete .github/CODEOWNERS * Added "Training" section to main readme with relative link to training materials * added info and link to APHL website for intermediate docker bioinformatics workshop --------- Co-authored-by: Andrew Lang <[email protected]>
StaPH-B · Sep 20, 2024 · 9cc6d2a · 9cc6d2a
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diff --git a/.gitpod.yml b/.gitpod.yml
@@ -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

diff --git a/README.md b/README.md
@@ -90,6 +90,11 @@ 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/)
+- Video training from APHL 2024 workshop **Intermediate Docker Bioinformatics Workshop** can be located in [APHL's e-learning resources](https://learn.aphl.org/learn/course/external/view/elearning/355/intermediate-docker-bioinformatics-workshop)
+
 ## 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)

diff --git a/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 1 - Lecture.pptx.pdf b/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 1 - Lecture.pptx.pdf
diff --git a/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 2 - Lecture.pptx.pdf b/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 2 - Lecture.pptx.pdf
diff --git a/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 3 - Lecture.pptx.pdf b/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 3 - Lecture.pptx.pdf
diff --git a/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 4 - Lecture.pptx.pdf b/...er-for-PH-bioinformatics-May2023/Intro to Docker for PH Bioinfo Week 4 - Lecture.pptx.pdf