From 6156fb397f6e6cea57c902f3bbd07f39cf8423ed Mon Sep 17 00:00:00 2001
From: Jeanne Cheneby <jeannech@uio.no>
Date: Tue, 5 Nov 2024 10:48:25 +0100
Subject: [PATCH] feat: include entrypoint into docker

---
 Dockerfile    |  7 +++++++
 entrypoint.sh | 19 +++++++++++++++++++
 2 files changed, 26 insertions(+)
 create mode 100755 entrypoint.sh

diff --git a/Dockerfile b/Dockerfile
index 160217c..ee32af5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -46,6 +46,11 @@ RUN chown -R galaxy:galaxy /database
 RUN mkdir /study
 RUN chown 777 /study
 
+# Import the entrypoint script
+COPY entrypoint.sh /entrypoint.sh
+RUN  chmod +x /entrypoint.sh
+RUN  chown galaxy:galaxy /entrypoint.sh
+
 # switch back to galaxy
 USER galaxy
 
@@ -65,3 +70,5 @@ RUN sed -i 's|^[[:space:]]*tool_dependency_dir:.*|#&|' config/galaxy.yml
 RUN pip install pandas matplotlib seaborn numpy scipy galaxy-lib numba dsnparse mysqlclient python-dotenv
 
 
+
+
diff --git a/entrypoint.sh b/entrypoint.sh
new file mode 100755
index 0000000..6aa7ffb
--- /dev/null
+++ b/entrypoint.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Clear the set_env.sh file
+touch /galaxy/server/tools/plot_clusters_prevalence/.env
+
+# Write the environment variables into the set_env.sh file
+echo "UPLOAD_IMAGE_ENDPOINT=${UPLOAD_IMAGE_ENDPOINT}" >> /galaxy/server/tools/export_cbioportal_image/.env
+echo "CBIOPORTAL_LOAD_RESOURCE_ENDPOINT=${CBIOPORTAL_LOAD_RESOURCE_ENDPOINT}" >> /galaxy/server/tools/export_cbioportal_image/.env
+echo "IMAGE_BASE_URL=${IMAGE_BASE_URL}" >> /galaxy/server/tools/export_cbioportal_image/.env
+
+touch /galaxy/server/tools/export_cbioportal_timeline/.env
+
+echo "EXPORT_TIMELINE_ENDPOINT=${EXPORT_TIMELINE_ENDPOINT}" >> /galaxy/server/tools/export_cbioportal_timeline/.env
+
+
+
+
+# Pass control to the default command or any other command specified
+exec "$@"