fixes

Author: johanneskoester

.gitpod.yml

@@ -6,10 +6,11 @@ tasks:
       rm Dockerfile
       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 "PS1='\w\$ '" >> ~/.bashrc
-      source ~/.bashrc
       echo "*" > .gitignore
-      conda activate snakemake-tutorial
+      conda init
+      source ~/.bashrc
       clear
+      conda activate snakemake-tutorial
 
 vscode:
   extensions:

Dockerfile

@@ -1,5 +1,6 @@
 FROM snakemake/snakemake:stable
 ADD environment.yaml .
-RUN grep -v snakemake-minimal environment.yaml > /tmp/environment.yaml; mamba env update -n snakemake -f /tmp/environment.yaml
+RUN mamba create -n snakemake-tutorial --clone snakemake; \
+    mamba env update -n snakemake-tutorial -f environment.yaml;
 RUN mkdir -p /tmp/conda
 ENV CONDA_PKGS_DIRS /tmp/conda