[ALS-5982] Move conda env config to install_kernel script (#170)

hms-dbmi · Mar 1, 2024 · ff5c722 · ff5c722
1 parent e83cfea
commit ff5c722
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Showing 3 changed files with 14 additions and 12 deletions.
diff --git a/main/solution/post-deployment/config/environment-files/environments/sagemaker.sh b/main/solution/post-deployment/config/environment-files/environments/sagemaker.sh
@@ -1,17 +1,5 @@
 #!/usr/bin/env bash
 
-# --------------------------- Load Kernels to Conda -------------------------- #
-KERNEL_PATH="/home/ec2-user/SageMaker/.kernels"
-echo "Adding $KERNEL_PATH to conda configuration"
-mkdir -p $KERNEL_PATH
-chown ec2-user:ec2-user $KERNEL_PATH
-cat << EOF >> /home/ec2-user/.condarc
-envs_dirs:
-  - $KERNEL_PATH
-  - /home/ec2-user/anaconda3/envs
-EOF
-echo "Finished Adding $KERNEL_PATH to conda configuration"
-
 # --------------------------------- Idle Stop -------------------------------- #
 if [ "$AUTO_STOP_IDLE_TIME" != "0" ]; then
   echo "Installing the idle stop script"

diff --git a/main/solution/post-deployment/config/environment-files/get_bootstrap.sh b/main/solution/post-deployment/config/environment-files/get_bootstrap.sh
@@ -1,4 +1,7 @@
 #!/usr/bin/env bash
+
+# DEPRECATED - use bootstrap.sh instead
+
 bootstrap_s3_location="$1"
 s3_mounts="$2"
 

diff --git a/main/solution/post-deployment/config/environment-files/install_kernel.sh b/main/solution/post-deployment/config/environment-files/install_kernel.sh
@@ -23,3 +23,14 @@ if [ "$kernels" != "" ]; then
     fi
   done
 fi
+
+# --------------------------- Load Kernels to Conda -------------------------- #
+echo "Adding $KERNEL_PATH to conda configuration"
+mkdir -p $KERNEL_PATH
+chown ec2-user:ec2-user $KERNEL_PATH
+cat << EOF >> /home/ec2-user/.condarc
+envs_dirs:
+  - $KERNEL_PATH
+  - /home/ec2-user/anaconda3/envs
+EOF
+echo "Finished Adding $KERNEL_PATH to conda configuration"