diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..47aaa51 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,9 @@ +// For format details, see https://aka.ms/devcontainer.json. +{ + "name": "Snakemake-Tutorial", + "build": { + "context": "..", + "dockerfile": "../Dockerfile" + }, + "postCreateCommand": "bash .devcontainer/setup.bash" +} diff --git a/.devcontainer/setup.bash b/.devcontainer/setup.bash new file mode 100644 index 0000000..ff66de6 --- /dev/null +++ b/.devcontainer/setup.bash @@ -0,0 +1,14 @@ +#!/usr/bin/env bash +# abort on error, undefined vars, and failed pipelines +set -euo pipefail + +rm -f Dockerfile .gitpod.yml && rm -rf .github .devcontainer +echo -e "# Snakemake-Tutorial\n\nYour gitpod workspace for the snakemake-tutorial has been initialized. Now you can start with the [basic tutorial](https://snakemake.readthedocs.io/en/stable/tutorial/basics.html)." > README.md +echo "*" > .gitignore +conda init +set +u +source ~/.bashrc +set -u + +echo 'conda activate snakemake-tutorial' >> ~/.bashrc +echo "Setup done"