From 50926bced16017b9a66881d3769e0d8256f0b259 Mon Sep 17 00:00:00 2001 From: Ubuntu Date: Tue, 29 Aug 2017 21:20:58 +0000 Subject: [PATCH 1/2] make parent uuids a list and not string make parent uuids a list and not string --- DockstoreRunner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DockstoreRunner.py b/DockstoreRunner.py index a70972b..c93b763 100644 --- a/DockstoreRunner.py +++ b/DockstoreRunner.py @@ -467,7 +467,7 @@ def run(self): { "version" : "1.0.0", "timestamp" : "%s", - "parent_uuids" :"%s", + "parent_uuids" : %s, "workflow_url" : "%s", "workflow_name" : "%s", "workflow_version" : "%s", From f37d270130020efa4be55f8ea23e194d59737730 Mon Sep 17 00:00:00 2001 From: Ubuntu Date: Tue, 29 Aug 2017 21:30:10 +0000 Subject: [PATCH 2/2] bump tool runner version bump tool runner version --- Dockstore.cwl | 2 +- README.md | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockstore.cwl b/Dockstore.cwl index 8f24126..1d4acbb 100644 --- a/Dockstore.cwl +++ b/Dockstore.cwl @@ -24,7 +24,7 @@ dct:creator: requirements: - class: DockerRequirement - dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.19" + dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20" hints: - class: ResourceRequirement diff --git a/README.md b/README.md index 24484c1..c3063a3 100644 --- a/README.md +++ b/README.md @@ -99,7 +99,7 @@ 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:1.0.19 . + docker build -t quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20 . # fill in your JSON from Dockstore.json template as Dockstore.my.json mkdir /datastore; chown ubuntu:ubuntu /datastore/ # local execution @@ -107,7 +107,7 @@ Most people, other than developers of this tool, will use the Dockstore CLI to i # 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:1.0.19 --json Dockstore.my.json + dockstore tool launch --entry quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20 --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