readme file

Author: qu-y

.github/templates/README-sysbio-portal.md

@@ -0,0 +1,40 @@
+# SysBio Portal Code
+
+This repository contains the code for the SysBio Portal, automatically synced from the source repository.
+
+**Please do not make direct edits here.** Changes should be made in the source repository. Contact the maintainers for any questions. This is WIP repo, and depends on how things progress, auto-sync might be disabled in favor of manual review in the future if needed.
+
+To set the volcano plot to a different data source (in the gene expression browser), you can set the environment variable `VUE_APP_VOLCANO_DATASET_URL` to desired path at runtime.
+
+To run: `npm install`, then `npm run deploy`
+
+The output will be in the `portals/SysBio` directory, ready to be served by any webserver.
+
+## Docker Support
+
+This repository includes Docker support for easy deployment:
+
+```bash
+# Build and run with Docker Compose
+docker-compose up -d
+
+# Or build and run with Docker directly
+docker build -t sysbio-portal .
+docker run -p 8080:8080 sysbio-portal
+```
+
+The application will be available at http://localhost:8080
+
+### Build-time Configuration
+
+Environment variables can be set at build time:
+
+```bash
+# Using Docker build args
+docker build --build-arg VUE_APP_VOLCANO_DATASET_URL=https://example.com/data.csv.gz -t sysbio-portal .
+
+# Using Docker Compose
+# Edit docker-compose.yml to include your desired build args
+```
+
+For more detailed Docker instructions, see `DOCKER_README.md`.

.github/workflows/sysbio-code-sync.yml

@@ -52,18 +52,7 @@ jobs:
             # Step 4.5: Create a custom README in the target directory
             - name: Create Custom README in Target
               run: |
-                  echo "# SysBio Portal Code" > repo-b/README.md
-                  echo "" >> repo-b/README.md
-                  echo "This repository contains the code for the SysBio Portal, automatically synced from the source repository." >> repo-b/README.md
-                  echo "" >> repo-b/README.md
-                  echo "**Please do not make direct edits here.** Changes should be made in the source repository. Contact the maintainers for any questions. This is WIP repo, and depends on how things progress, auto-sync might be disabled in favor of manual review in the future if needed." >> repo-b/README.md
-                  echo "" >> repo-b/README.md
-                  echo "" >> repo-b/README.md
-                  echo "To set the volcano plot to a different data source (in the gene expression browser), you can set the environment variable \`VUE_APP_VOLCANO_DATASET_URL\` to desired path at runtime." >> repo-b/README.md
-                  echo "" >> repo-b/README.md
-                  echo "To run: \`npm install\`, then \`npm run deploy\`" >> repo-b/README.md
-                  echo "" >> repo-b/README.md
-                  echo "The output will be in the \`portals/SysBio\` directory, ready to be served by any webserver." >> repo-b/README.md
+                  cp .github/templates/README-sysbio-portal.md repo-b/README.md
 
             # Step 4.6: Replace vue.config.js with configs/vue.config.SysBio.js in the target directory
             - name: Update Vue config in target