Bugfix/docker env (#201)

* update docker container to activate micromamba env correctly
geoschem · Apr 11, 2024 · 01492f3 · 01492f3
1 parent 460985d
commit 01492f3
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diff --git a/resources/containers/base-image/install-scripts/install-micromamba.sh b/resources/containers/base-image/install-scripts/install-micromamba.sh
@@ -16,4 +16,4 @@ echo "export MAMBA_ROOT_PREFIX=/opt/micromamba" >> /etc/bashrc
 echo 'eval "$(/opt/micromamba/bin/micromamba shell hook -s posix)"' >> /etc/bashrc
 
 # set alias to use conda and micromamba interchangeably
-echo "alias conda='micromamba'" >> /etc/bashrc
+echo $'conda() {\n    micromamba "$@"\n}' >> /etc/bashrc
diff --git a/resources/containers/container_config.yml b/resources/containers/container_config.yml
@@ -175,7 +175,7 @@ OutputPath: "/home/al2/imi_output_dir"
 DataPath: "/home/al2/ExtData"
 
 ## Conda environment files
-CondaFile: "/opt/conda/etc/profile.d/conda.sh"
+CondaFile: "/etc/bashrc"
 CondaEnv: "imi_env"
 
 ## Download initial restart file from AWS S3?

diff --git a/resources/containers/entrypoint.sh b/resources/containers/entrypoint.sh
@@ -55,8 +55,7 @@ if [[ "x${IMI_CONFIG_PATH}" != "x" ]]; then
 else
 	config_file="config.yml"
 	# remove default config file and replace with docker config file
-	rm config.yml
-	mv resources/containers/container_config.yml config.yml
+	cp resources/containers/container_config.yml config.yml
 fi
 
 # override specific config file vars with env variables of