[ARVADOS] updated: 274e832a7ae7bcddd3c6a98863f8b2c46597c881
Git user
git at public.curoverse.com
Wed Mar 2 09:05:21 EST 2016
Summary of changes:
sdk/cwl/arvados_cwl/__init__.py | 1 +
sdk/cwl/setup.py | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
via 274e832a7ae7bcddd3c6a98863f8b2c46597c881 (commit)
from 8408c834128282437ad1741b17e5221f0eef7da4 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 274e832a7ae7bcddd3c6a98863f8b2c46597c881
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 2 08:46:41 2016 -0500
8488: Set docker_outdir to get correct outdir in command line. Bump cwltool
dependency to get better workflow iteration.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 105d754..6429a91 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -367,6 +367,7 @@ class ArvCwlRunner(object):
jobiter = tool.job(job_order,
input_basedir,
self.output_callback,
+ docker_outdir="$(task.outdir)",
**kwargs)
try:
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 3fe4e16..cdbb41b 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -30,7 +30,7 @@ setup(name='arvados-cwl-runner',
'bin/arvados-cwl-runner'
],
install_requires=[
- 'cwltool>=1.0.20160225202307',
+ 'cwltool>=1.0.20160302134341',
'arvados-python-client>=0.1.20160219154918'
],
zip_safe=True,
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list