Merge branch 'release/1.0.18'

Author: Walt Shands

Dockstore.cwl

@@ -24,7 +24,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.17"
+    dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.18"
 
 hints:
   - class: ResourceRequirement

DockstoreRunner.py

@@ -467,16 +467,14 @@ def run(self):
 {
    "version" : "1.0.0",
    "timestamp" : "%s",
-   "parent_uuids" : [
-      "%s"
-   ],
+   "parent_uuids" :"%s",
    "workflow_url" : "%s",
    "workflow_name" : "%s",
    "workflow_version" : "%s",
    "analysis_type" : "%s",
    "bundle_uuid" : "%s",
    "workflow_params" : {
-''' % (str(utc_datetime.isoformat("T")), self.parent_uuids, self.dockstore_url, self.workflow_name, self.workflow_version, self.workflow_type, self.bundle_uuid)
+''' % (str(utc_datetime.isoformat("T")), self.parent_uuids.split(","), self.dockstore_url, self.workflow_name, self.workflow_version, self.workflow_type, self.bundle_uuid)
         i=0
         (params_map, file_input_map) = self.map_params(transformed_json_path)
         params_map_keys = params_map.keys()

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:1.0.17 .
+    docker build -t quay.io/ucsc_cgl/dockstore-tool-runner:1.0.18 .
     # 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:1.0.17 --json Dockstore.my.json
+    dockstore tool launch --entry quay.io/ucsc_cgl/dockstore-tool-runner:1.0.18 --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