diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2696b31df..d5a82399a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -404,6 +404,7 @@ end-to-end-core-setup:
     - random_string=$(bash -c "cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w "10" | head -n 1")
     - >
       cat <<EOF > run_web.sh
+      #!/bin/bash
       docker run -d
       --name "core-${BRANCH_LOWER}-${CI_COMMIT_SHORT_SHA}-${random_string}"
       -e DATAFED_GLOBUS_APP_SECRET="$CI_DATAFED_GLOBUS_APP_SECRET"
@@ -449,6 +450,8 @@ end-to-end-repo-setup:
     - ./scripts/container_stop.sh -t "${REGISTRY}/${IMAGE_TAG}${BRANCH_LOWER}"
     - random_string=$(bash -c "cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w "10" | head -n 1")
     - >
+      cat <<EOF > run_repo.sh
+      #!/bin/bash
       docker run -d
       --name "repo-${BRANCH_LOWER}-${CI_COMMIT_SHORT_SHA}-${random_string}"
       -e DATAFED_GLOBUS_APP_SECRET="$CI_DATAFED_GLOBUS_APP_SECRET"
@@ -461,6 +464,9 @@ end-to-end-repo-setup:
       -v "$CI_DATAFED_REPO_PRIV_KEY":/source/install/keys/datafed-repo-key.priv
       -t "${REGISTRY}/${IMAGE_TAG}${BRANCH_LOWER}" 
        </dev/null &>/dev/null &
+       EOF
+    - chmod +x run_repo.sh
+    - ./run_repo.sh
     - sleep 10
     - ./scripts/container_run_test.sh -e -c "1" -t "${REGISTRY}/${IMAGE_TAG}${BRANCH_LOWER}" 
 
@@ -484,6 +490,8 @@ end-to-end-gcs-authz-setup:
     - ./scripts/container_stop.sh -t "${REGISTRY}/${IMAGE_TAG}${BRANCH_LOWER}"
     - random_string=$(bash -c "cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w "10" | head -n 1")
     - >
+      cat <<EOF > run_globus.sh
+      #!/bin/bash
       docker run -d
       --name "gcs-authz-${BRANCH_LOWER}-${CI_COMMIT_SHORT_SHA}-${random_string}"
       -e DATAFED_GLOBUS_APP_SECRET="$CI_DATAFED_GLOBUS_APP_SECRET"
@@ -496,6 +504,9 @@ end-to-end-gcs-authz-setup:
       -v "$CI_DATAFED_REPO_PRIV_KEY":/source/install/keys/datafed-repo-key.priv
       -t "${REGISTRY}/${IMAGE_TAG}${BRANCH_LOWER}" 
        </dev/null &>/dev/null &
+       EOF
+    - chmod +x run_globus.sh
+    - ./run_globus.sh
     - sleep 10
     - ./scripts/container_run_test.sh -e -c "1" -t "${REGISTRY}/${IMAGE_TAG}${BRANCH_LOWER}"