Merge pull request #39 from SD2E/maverick_migration

Maverick migration

Author: wjallen

docs/03.migrate_from_maverick.md

@@ -0,0 +1,65 @@
+---
+layout: page
+title: Migrating Apps from Maverick
+tagline:
+---
+
+With Maverick reaching the end of its service, we will need to migrate apps off of Maverick onto another HPC resource. Luckily, due to containerization, this process is pretty painless. You will simply need to replace the `executionSystem` in the app definition (app.json.j2) from `hpc-tacc-maverick-username` to the newly created `hpc-tacc-wranlger-username`.
+
+
+<br>
+#### Example of an Updated App Definition
+
+This is an example of a converted Agave app definition:
+{% raw %}
+```json
+{
+  "name": "{{ agave.username }}-{{ app.name }}",
+  "version": "{{ app.version }}",
+  "executionType": "HPC",
+  "executionSystem": "hpc-tacc-wrangler-{{ agave.username }}",
+  "parallelism": "SERIAL",
+  "deploymentPath": "{{ agave.username }}/apps/{{ app.name }}-{{ app.version }}",
+  "deploymentSystem": "data-sd2e-projects-users",
+  "defaultProcessorsPerNode": 1,
+  "defaultNodeCount": 1,
+  "defaultQueue": "normal",
+  "label": "FastQC",
+  "modules": [ "load tacc-singularity" ],
+  "shortDescription": "A Quality Control application for FastQ files",
+  "templatePath": "runner-template.sh",
+  "testPath": "tester.sh",
+  "inputs": [
+    {
+      "id": "fastq",
+      "value": {
+        "default": "agave://data-sd2e-community/sample/sailfish/test/read1.fastq",
+        "visible": true,
+        "required": true
+      },
+      "details": {
+        "label": "FASTQ sequence file"
+      },
+      "semantics": {
+        "ontology": [ "http://edamontology.org/format_1930" ]
+      }
+    }
+  ],
+  "parameters": [],
+  "outputs": []
+}
+```
+{% endraw %}
+
+#### Final steps
+After updating the app definition to point to `hpc-tacc-wrangler-username`, you can simply run `apps-deploy` to deploy the app to the new execution system. Make sure to double check the `app.ini` file to ensure it points to the correct DockerHub username, repo, app name, and app version. If the app name and version in the app.ini differ from the name/version of the app directory, you can use a -F flag with `apps-deploy` to point to the correct app definition, ex:
+```
+apps-deploy -F app_directory-0.1.1/app.json.j2
+```
+Once the application has been deployed you should run a test job to ensure it's working correctly.
+
+
+
+
+---
+Return to the [API Documentation Overview](../index.md)

index.md

@@ -57,6 +57,8 @@ the SD2E platform. Documentation for getting started with the SD2E API is below.
 
     3.5 [Old App Building Process](docs/old/03.old_create_app.md) (*deprecated*)
 
+    3.6 [Migrate Apps from Maverick](docs/03.migrate_from_maverick.html)
+
 
   **4 Abaco Reactors**