Initial commit

.github/workflows/pages.yml

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+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll with GitHub Pages dependencies preinstalled
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Pages
+        uses: actions/configure-pages@v1
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./website
+          destination: ./website/_site
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: ./website/_site
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.gitignore

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+modules/02-sequencing/data
+modules/02-sequencing/ref
+modules/02-sequencing/tmp
+**/*.h5ad
+**/*.ipynb_checkpoints

.gitmodules

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+[submodule "07-softengteam"]
+	path = modules/07-softengteam
+	url = https://github.com/bioinfo-ucsd/BISB-Bootcamp-2022-module-07
+[submodule "docker"]
+	path = docker
+	url = https://github.com/ucsd-ets/BNFO000.git
+[submodule "modules/02-softengteam"]
+	path = modules/02-softengteam
+	url = https://github.com/bioinfo-ucsd/BISB-Bootcamp-module-07

README.md

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+# BISB Bootcamp 2023
+
+This is the course repository for the 2023 UC San Diego Bioinformatics & Systems Biology (BISB) PhD program Bootcamp. To learn more about bootcamp, please visit the [course website](https://bioinfo-ucsd.github.io/BISB-Bootcamp-2023/).
+
+This repo is structured as follows:
+
+```bash
+.
+├── README.md # this file
+├── website # course website
+└── modules # materials for each module
+```
+
+To contribute to the course website, please follow the instructions at [./docs/README.md](./docs/README.md).
+
+To contribute to the course materials, please follow the instructions at [./modules/README.md](./modules/README.md).
+
+## Adapting this repository for future iterations of BISB Bootcamp
+
+Click [Use this template](https://github.com/bioinfo-ucsd/BISB-Bootcamp-2023/generate) to create a new repo for a future bootcamp. Then edit away!

dope.txt

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+data science is rad

env.yml

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+name: bootcamp
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  # general use
+  - conda-forge::gh
+  - conda-forge::awscli
+  - conda-forge::wget
+  - conda-forge::nbconvert
+  - conda-forge::tree
+  # Command Line
+  - bioconda::samtools>=1.15
+  - bioconda::bcftools>=1.15
+  - bioconda::bedtools>=2.30.0
+  - bioconda::picard>=2.27.4
+  - bioconda::gatk4
+  - bioconda::fastqc
+  - bioconda::multiqc
+  # Python
+  - conda-forge::python>=3.7
+  - conda-forge::pip
+  - conda-forge::biopython
+  - conda-forge::ipykernel
+  - conda-forge::numpy<=1.21
+  - conda-forge::pandas
+  - conda-forge::scanpy
+  # R
+  - conda-forge::r-base>=4.0
+  - conda-forge::r-essentials
+  - conda-forge::r-irkernel
+  # pip
+  - pip:
+    - igv-notebook

modules/.gitignore

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+.ipynb_checkpoints**