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Update gitpod #285

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Nov 29, 2024
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20 changes: 14 additions & 6 deletions .gitpod.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,20 +11,28 @@
image: nfcore/gitpod:latest

tasks:
- name: Install Pixi
- name: Init Conda and Install Pixi
command: |
sudo chown gitpod -R /home/gitpod/
# Conda setup
export CONDA_ENVS_PATH=/workspace/conda/envs
conda config --set repodata_threads 4
conda config --set auto_activate_base false
conda config --remove channels defaults
conda init
conda env create -f tutorials/jupyter/environment.yml
conda env create -f tutorials/nextflow/environment.yml
conda env create -f tutorials/quarto/environment.yml
conda env create -f tutorials/snakemake/environment.yml
# Install Pixi
curl -fsSL https://pixi.sh/install.sh | bash
. /home/gitpod/.bashrc
echo sourced /home/gitpod/.bashrc
conda env list
- name: Update Nextflow
command: |
nextflow self-update
exit
- name: Install Snakemake and Quarto
command: |
conda install snakemake quarto -y
exit


vscode:
extensions:
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1 change: 1 addition & 0 deletions tutorials/quarto/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ channels:
- conda-forge
- bioconda
dependencies:
- quarto
- jupyter
- python=3
- r-base
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