[ARVADOS] updated: 274e832a7ae7bcddd3c6a98863f8b2c46597c881

[Git user]

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)

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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,

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