Create .dockstore.yml

Author: denis-yuen

.dockstore.yml

@@ -0,0 +1,77 @@
+# .dockstore.yml for Xena
+version: 1.1
+service:
+  type: docker-compose
+  name: UCSC Xena Browser
+  author: UCSC Genomics Institute
+  description: |
+    The UCSC Xena browser is an exploration tool for public and private,
+    multi-omic and clinical/phenotype data.
+    It is recommended that you configure a reverse proxy to handle HTTPS
+  # These are files the Dockstore will index. They will be directly downloadable from Dockstore
+  files:
+     - docker-compose.yml
+     - README.md
+     - stand_up.sh
+     - load.sh
+     - port.sh
+     - stop.sh
+
+  scripts:
+    # The scripts preprovision, prestart, start, poststart, and postprovision will be executed in order.
+    # The only script required to have a value is start.
+
+    # Before any provisioning
+    preprovision:
+
+    # After provisioning, before starting the service
+    prestart:
+
+    # Starts the service
+    start: stand_up.sh
+
+    # After the service has started
+    poststart:
+
+    # After the service has started. For multiple provisionings, e.g., the user may decide to add more data later.
+    postprovision: load.sh
+
+    # Returns the port the service is exposing. Can be used by a client to know what port to proxy
+    port: port.sh
+
+    # Returns an exit code of 0 if service is running successfully.
+    healthcheck:
+
+    # Stops the service
+    stop: stop.sh
+
+  # Items in this section are passed to the scripts as environment variables.
+  # The names must be valid enviornment variable names.
+  environment:
+    httpPort: # The name of the environment variable
+        default: "7222" # An optional default value
+        # A description that tools can use for prompting a user.
+        description: The host's HTTP port. The default is 7222.
+
+  # Data are files that are provisioned locally for the service. Each key is a dataset name,
+  # and each dataset can contain 1 to n files
+  data:
+    # The name of a dataset, can be anything
+    dataset_1:
+        # The location on the local system where files should be downloaded to. This
+        # can be overriden if desired on an individual file level.
+        # In this case, Xena requires files to be located in the subdirectory xena/files
+        # relative to where Xena is running.
+        targetDirectory: xena/files 
+
+        # The files property is required for datasets. It contains one or more files.
+        # The sets of files can be repeated. In the sample xena-all.json, there are
+        # 3 pairs of tsv/metadata files.
+        files:
+            tsv:
+                description: Data for Xena in TSV format
+
+                # Could override targetDirectory here, but since all files go into xena/files, no need
+                # targetDirectory:
+            metadata:
+                description: The metadata, in JSON format, that corresponds to the previous tsv file