Merge pull request #40 from Sydney-Informatics-Hub/gitpod

Open directory in vs explorer

.gitpod.code-workspace

@@ -1,7 +1,7 @@
 {
   "folders": [
     {
-      "path": "./hello-nextflow"  // Opens the correct directory in the explorer
+      "path": "/workspace/hello-nextflow"  // Opens the correct directory in the explorer
     }
   ],
   "settings": {

README.md

@@ -1,136 +1,14 @@
 # hello-nextflow
-Training materials for a Nextflow beginners workshop 2024
 
-Content published on: [https://sydney-informatics-hub.github.io/hello-nextflow/](https://sydney-informatics-hub.github.io/hello-nextflow/)
+Training materials for SIH's implementation of Seqera's Hello Nextflow workshop 2024.
 
-## VM Installation (for users)  
+Event description [here](https://www.biocommons.org.au/events/hello-nextflow).
 
-See [vm_install/](/vm_install).  
+Content published at: [https://sydney-informatics-hub.github.io/hello-nextflow/](https://sydney-informatics-hub.github.io/hello-nextflow/)
 
-## Developer Installation  
+## Self-directed materials
+[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/<your-username>/<your-repo>)
 
-### `mamba`  
-
-```bash
-wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
-bash Miniforge3-$(uname)-$(uname -m).sh
-# complete prompts with defaults
-
-export PATH="$HOME/miniforge3/bin:$PATH"
-source ~/.bashrc
-
-# confirm installation versions
-mamba --version
-```
-
-```console
-mamba 1.5.8
-conda 24.3.0
-```
-
-Install packages:  
-
-```bash
-mamba create -n day2
-mamba activate day2
-mamba install -c bioconda nextflow # process tools via docker containers
-mamba install -c conda-forge mkdocs mkdocs-material
-```
-
-```bash
-mamba list | grep -E "nextflow|mkdocs |mkdocs-material"
-```
-
-```console
-mkdocs                    1.6.0              pyhd8ed1ab_0    conda-forge
-mkdocs-material           9.5.31             pyhd8ed1ab_0    conda-forge
-mkdocs-material-extensions 1.3.1              pyhd8ed1ab_0    conda-forge
-nextflow                  24.04.4              hdfd78af_0    bioconda
-```
-
-### Docker   
-
-Follows [ubuntu installation](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository) and [linux post-install steps](https://docs.docker.com/engine/install/linux-postinstall/).
-
-```bash
-# Add Docker's official GPG key:
-sudo apt update
-sudo apt install ca-certificates curl
-sudo install -m 0755 -d /etc/apt/keyrings
-sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
-sudo chmod a+r /etc/apt/keyrings/docker.asc
-
-# Add the repository to Apt sources
-echo \
-  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
-  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
-  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
-
-sudo apt update
-
-# Install the latgest Docker packages
-sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
-
-# Check installed correctly
-sudo docker run hello-world
-
-# post-install mods for non-root permissions
-sudo groupadd docker
-sudo usermod -aG docker $USER
-newgrp docker
-
-# confirm user access
-docker run hello-world
-```
-
-#### Pull containers  
-
-```bash
-docker pull quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0
-docker pull quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0
-docker pull quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0
-```
-
-## Developer Usage
-
-### VM testing  
-
-#### Part 1
-```
-nextflow run nextflow-io/hello
-```
-
-#### Part 2
-
-**Note:** `.main.nf` and `.nextflow.config` runs the final pipeline. 
-
-```bash
-git clone https://github.com/Sydney-Informatics-Hub/hello-nextflow.git
-cd hello-nextflow/part2  
-mv .nextflow.config nextflow.config
-```
-
-Run completed pipeline (includes introspection reports etc., multi-sample and multiple cpus):  
-
-```bash
-nextflow run .main.nf --reads data/samplesheet_full.csv
-```
-
-### mkdocs  
-
-To generate html docs during development (before deploying):
-
-```bash
-cd ~/hello-nextflow/
-mkdocs serve
-# open http://127.0.0.1:8000/ in browser
-```
-
-To render docs for website (manually):  
-
-```bash
-mkdocs gh-deploy
-```
-
-Open [https://sydney-informatics-hub.github.io/hello-nextflow/](https://sydney-informatics-hub.github.io/hello-nextflow/) in a browser.  
+## Developers 
 
+See [set up instructions](./dev_setup/README.md)

dev_setup/README.md

@@ -0,0 +1,9 @@
+# Developer instructions 
+
+## Environment set up
+
+See [dev environment setup instrucitons](dev_setup.md)
+
+## Nectar VM installation  
+
+See [VM install instructions](vm_install.md)

dev_setup/dev_setup.md

@@ -0,0 +1,128 @@
+
+# Developer Installation  
+
+## `mamba`  
+
+```bash
+wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+bash Miniforge3-$(uname)-$(uname -m).sh
+# complete prompts with defaults
+
+export PATH="$HOME/miniforge3/bin:$PATH"
+source ~/.bashrc
+
+# confirm installation versions
+mamba --version
+```
+
+```console
+mamba 1.5.8
+conda 24.3.0
+```
+
+Install packages:  
+
+```bash
+mamba create -n day2
+mamba activate day2
+mamba install -c bioconda nextflow # process tools via docker containers
+mamba install -c conda-forge mkdocs mkdocs-material
+```
+
+```bash
+mamba list | grep -E "nextflow|mkdocs |mkdocs-material"
+```
+
+```console
+mkdocs                    1.6.0              pyhd8ed1ab_0    conda-forge
+mkdocs-material           9.5.31             pyhd8ed1ab_0    conda-forge
+mkdocs-material-extensions 1.3.1              pyhd8ed1ab_0    conda-forge
+nextflow                  24.04.4              hdfd78af_0    bioconda
+```
+
+## Docker   
+
+Follows [ubuntu installation](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository) and [linux post-install steps](https://docs.docker.com/engine/install/linux-postinstall/).
+
+```bash
+# Add Docker's official GPG key:
+sudo apt update
+sudo apt install ca-certificates curl
+sudo install -m 0755 -d /etc/apt/keyrings
+sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
+sudo chmod a+r /etc/apt/keyrings/docker.asc
+
+# Add the repository to Apt sources
+echo \
+  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
+  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
+  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+
+sudo apt update
+
+# Install the latgest Docker packages
+sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+
+# Check installed correctly
+sudo docker run hello-world
+
+# post-install mods for non-root permissions
+sudo groupadd docker
+sudo usermod -aG docker $USER
+newgrp docker
+
+# confirm user access
+docker run hello-world
+```
+
+### Pull containers  
+
+```bash
+docker pull quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0
+docker pull quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0
+docker pull quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0
+```
+
+## Developer Usage
+
+### VM testing  
+
+#### Part 1
+```
+nextflow run nextflow-io/hello
+```
+
+#### Part 2
+
+**Note:** `.main.nf` and `.nextflow.config` runs the final pipeline. 
+
+```bash
+git clone https://github.com/Sydney-Informatics-Hub/hello-nextflow.git
+cd hello-nextflow/part2  
+mv .nextflow.config nextflow.config
+```
+
+Run completed pipeline (includes introspection reports etc., multi-sample and multiple cpus):  
+
+```bash
+nextflow run .main.nf --reads data/samplesheet_full.csv
+```
+
+## mkdocs  
+
+To generate html docs during development (before deploying):
+
+```bash
+cd ~/hello-nextflow/
+mkdocs serve
+# open http://127.0.0.1:8000/ in browser
+```
+
+To render docs for website (manually):  
+
+```bash
+mkdocs gh-deploy
+```
+
+Open [https://sydney-informatics-hub.github.io/hello-nextflow/](https://sydney-informatics-hub.github.io/hello-nextflow/) in a browser.  
+