diff --git a/test/run-system-test.sh b/test/run-system-test.sh
index 6eddae2f2..e7754f3ac 100755
--- a/test/run-system-test.sh
+++ b/test/run-system-test.sh
@@ -17,22 +17,19 @@ BIN_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
 PACKAGE_DIR="${BIN_DIR%/*}"
 cd "${PACKAGE_DIR}/test"
 
-# Note: this doesn't work as a single command
-docker compose --env-file .env.test -p system-test down --volumes
+docker compose  -f docker-compose.yml  -f ../docker-compose.yml -p system-test down --volumes
+# Note: can't use an env file for multiple docker-compose files, so create in two commands
 docker compose --env-file .env.test -p system-test up -d --build --remove-orphans
-cd .. && \
-  docker compose --env-file test/.env.test -p system-test up -d --build && \
-  cd "${PACKAGE_DIR}/test"
+docker compose -f ../docker-compose.yml --env-file .env.test -p system-test up -d --build --remove-orphans
 
 ./scripts/insert_test_data.sh
 
 pip install -e "${PACKAGE_DIR}/pixl_core" && pip install -e "${PACKAGE_DIR}/cli"
-pixl populate "${PACKAGE_DIR}/test/resources/omop"
+pixl populate "resources/omop"
 pixl start
 sleep 65  # need to wait until the DICOM image is "stable" = 60s
 ./scripts/check_entry_in_pixl_anon.sh
 ./scripts/check_entry_in_orthanc_anon.sh
 ./scripts/check_max_storage_in_orthanc_raw.sh
 
-cd "${PACKAGE_DIR}"
-docker compose -f docker-compose.yml -f test/docker-compose.yml -p system-test down --volumes
+docker compose  -f docker-compose.yml  -f ../docker-compose.yml -p system-test down --volumes