Merge branch 'release/1.0.17'

Author: caaespin

Dockstore.cwl

@@ -24,7 +24,8 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.16"
+    dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.17"
+
 hints:
   - class: ResourceRequirement
     coresMin: 1
@@ -75,6 +76,12 @@ inputs:
     inputBinding:
       prefix: --workflow-type
 
+  launch_type:
+    type: string?
+    doc: "String that describes the launch type: tool or workflow"
+    inputBinding:
+      prefix: --launch-type
+
   parent_uuids:
     type: string
     doc: "UUIDs for parent"

DockstoreRunner.py

@@ -53,6 +53,9 @@ def __init__(self):
         parser.add_argument('--json-encoded', default='e30=', required=True)
         parser.add_argument('--docker-uri', default='quay.io/wshands/fastqc:latest', required=True)
         parser.add_argument('--dockstore-url', default='https://dockstore.org/containers/quay.io/wshands/fastqc', required=True)
+        parser.add_argument('--launch-type', default='tool', const='tool', nargs='?', 
+                         choices=['tool', 'workflow'], required=False, 
+                         help='run a workflow or tool (default: %(default)s)')
         parser.add_argument('--workflow-type', default='sequence_upload_qc_report', required=True)
         parser.add_argument('--parent-uuids', default='parent-UUID-dummy-value', required=True)
         # FIXME: this append seems to crash on the mac but it would be the way to go if we want multiple parents
@@ -84,6 +87,7 @@ def __init__(self):
         self.dockstore_url = args.dockstore_url
         self.workflow_name = args.docker_uri.split(':')[0]
         self.workflow_version = args.docker_uri.split(':')[1]
+        self.launch_type = args.launch_type
         self.workflow_type = args.workflow_type
         self.parent_uuids = args.parent_uuids
         self.bundle_uuid = uuid4()
@@ -447,7 +451,7 @@ def run(self):
         self.run_command(cmd, self.MAX_ATTEMPTS, self.DELAY_IN_SECONDS, True)
 
         print("Calling Dockstore to launch a Dockstore tool")
-        cmd = "dockstore tool launch --debug --entry "+self.docker_uri+" --json "+transformed_json_path
+        cmd = "dockstore " + self.launch_type + " launch --debug --entry "+self.docker_uri+" --json "+transformed_json_path
         self.run_command(cmd, self.MAX_PIPELINE_ATTEMPTS, self.DELAY_IN_SECONDS, cwd=self.tmp_dir)
 
         t_end = time.time()

README.md

@@ -99,15 +99,15 @@ Most people, other than developers of this tool, will use the Dockstore CLI to i
 
     # patch in /usr/local/lib/python2.7/dist-packages/cwltool
     # make a tmpdir like /datastore
-    docker build -t quay.io/ucsc_cgl/dockstore-tool-runner:1.0.16 .
+    docker build -t quay.io/ucsc_cgl/dockstore-tool-runner:1.0.17 .
     # fill in your JSON from Dockstore.json template as Dockstore.my.json
     mkdir /datastore; chown ubuntu:ubuntu /datastore/
     # local execution
     TMPDIR=/datastore dockstore tool launch --entry Dockstore.cwl --local-entry --json Dockstore.my.json
     # as root in /datastore
     TMPDIR=/datastore dockstore tool launch --entry ~ubuntu/gitroot/BD2KGenomics/dcc-dockstore-tool-runner/Dockstore.cwl --local-entry --json ~ubuntu/gitroot/BD2KGenomics/dcc-dockstore-tool-runner/Dockstore.my.json
     # execute published on dockstore (this is the way most people will use this tool!)
-    dockstore tool launch --entry quay.io/ucsc_cgl/dockstore-tool-runner:1.0.16 --json Dockstore.my.json
+    dockstore tool launch --entry quay.io/ucsc_cgl/dockstore-tool-runner:1.0.17 --json Dockstore.my.json
 
     # running you see it launch the cwltool command, you mind find this useful while debugging
     cwltool --enable-dev --non-strict --enable-net --outdir /datastore/./datastore/launcher-ff6b55b3-52e8-430c-9a70-1ff295332698/outputs/ --tmpdir-prefix /datastore/./datastore/launcher-ff6b55b3-52e8-430c-9a70-1ff295332698/working/ /home/ubuntu/gitroot/BD2KGenomics/dcc-dockstore-tool-runner/Dockstore.cwl /datastore/./datastore/launcher-ff6b55b3-52e8-430c-9a70-1ff295332698/workflow_params.json