From 55d7281025a0b220606d8c965c1cb01b5c49ee97 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 28 Nov 2024 14:36:46 +0000 Subject: [PATCH 1/2] Make Gitpod more like expected user environment --- .gitpod.yml | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index 0aeaddfa..834eb39c 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -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: From 27568b1abb4c8c65f634c2bf14f22567be3aba3e Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 28 Nov 2024 21:56:00 +0000 Subject: [PATCH 2/2] Add Quarto to quarto-env --- tutorials/quarto/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/tutorials/quarto/environment.yml b/tutorials/quarto/environment.yml index 36d5537a..5ab4daa4 100644 --- a/tutorials/quarto/environment.yml +++ b/tutorials/quarto/environment.yml @@ -3,6 +3,7 @@ channels: - conda-forge - bioconda dependencies: + - quarto - jupyter - python=3 - r-base