[ARVADOS] updated: d4a9835195f1c87d6d3436050d55bc60ba031259
Git user
git at public.curoverse.com
Thu Aug 11 16:30:37 EDT 2016
Summary of changes:
build/run-build-packages.sh | 2 +-
crunch_scripts/cwl-runner | 8 ++++++--
sdk/cwl/arvados_cwl/__init__.py | 22 ++++++++--------------
sdk/cwl/arvados_cwl/arvjob.py | 2 +-
sdk/cwl/arvados_cwl/fsaccess.py | 21 +++++++++++++++------
sdk/cwl/arvados_cwl/pathmapper.py | 5 ++---
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/arvados-tests.sh | 5 +++++
sdk/cwl/tests/arvados-tests.yml | 10 ++++++++++
sdk/cwl/tests/dir-job.yml | 3 +++
sdk/cwl/tests/keep-dir-test-input.cwl | 21 +++++++++++++++++++++
sdk/cwl/tests/runner.sh | 2 ++
sdk/cwl/tests/test_job.py | 4 +++-
.../tests/__init__.py => sdk/cwl/tests/testdir/a | 0
.../tests/__init__.py => sdk/cwl/tests/testdir/b | 0
.../tests/__init__.py => sdk/cwl/tests/testdir/c/d | 0
16 files changed, 78 insertions(+), 29 deletions(-)
create mode 100755 sdk/cwl/tests/arvados-tests.sh
create mode 100644 sdk/cwl/tests/arvados-tests.yml
create mode 100644 sdk/cwl/tests/dir-job.yml
create mode 100644 sdk/cwl/tests/keep-dir-test-input.cwl
create mode 100755 sdk/cwl/tests/runner.sh
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/testdir/a (100%)
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/testdir/b (100%)
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/testdir/c/d (100%)
via d4a9835195f1c87d6d3436050d55bc60ba031259 (commit)
via fd22b368fb9d3bdfa17d5b6a65279fde8664700e (commit)
via a4c37c079728f2013f5a299acc97f1b24c1e2884 (commit)
via bf43afc52fce505edbe3fad9daa6b0c729d02eeb (commit)
via 6e0abcdabb14bcd21695420d3cfab0d57362a2be (commit)
via 08698803d8b324ba9a889a3aa41559d782bcc4bf (commit)
via c961ea106e3528a2690f7ab1e0032fa68f650bfe (commit)
via 46df7c2b292e5f12da365b918b0f28757eb4c4ce (commit)
from 9dda943e37fce96c5debe1410a11cfa9c88daf48 (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 d4a9835195f1c87d6d3436050d55bc60ba031259
Merge: 9dda943 fd22b36
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 16:30:34 2016 -0400
Merge branch '9751-cwl-keep-dir' closes #9751
commit fd22b368fb9d3bdfa17d5b6a65279fde8664700e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 14:54:36 2016 -0400
9552: import compute_checksums from cwltool.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index f7792cd..fe3249c 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -27,6 +27,7 @@ from .fsaccess import CollectionFsAccess
from cwltool.process import shortname, UnsupportedRequirement
from cwltool.pathmapper import adjustFileObjs
+from cwltool.draft2tool import compute_checksums
from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
@@ -230,17 +231,7 @@ class ArvCwlRunner(object):
raise WorkflowException("Workflow did not return a result.")
if kwargs.get("compute_checksum"):
- def compute_checksums(fileobj):
- if "checksum" not in fileobj:
- checksum = hashlib.sha1()
- with self.fs_access.open(fileobj["location"], "rb") as f:
- contents = f.read(1024*1024)
- while contents != "":
- checksum.update(contents)
- contents = f.read(1024*1024)
- fileobj["checksum"] = "sha1$%s" % checksum.hexdigest()
-
- adjustFileObjs(self.final_output, compute_checksums)
+ adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
return self.final_output
commit a4c37c079728f2013f5a299acc97f1b24c1e2884
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 15:35:15 2016 -0400
9751: Fix handling local Directories
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index d258937..0970e72 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -91,11 +91,11 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
def listdir(self, fn): # type: (unicode) -> List[unicode]
collection, rest = self.get_collection(fn)
- if rest:
- dir = collection.find(rest)
- else:
- dir = collection
if collection:
+ if rest:
+ dir = collection.find(rest)
+ else:
+ dir = collection
return [abspath(l, fn) for l in dir.keys()]
else:
return super(CollectionFsAccess, self).listdir(fn)
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 7e9a159..e17264b 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -52,8 +52,8 @@ class ArvPathMapper(PathMapper):
elif srcobj["class"] == "Directory":
if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
- for l in srcobj["listing"]:
- self.visit(l, uploadfiles)
+ for l in srcobj["listing"]:
+ self.visit(l, uploadfiles)
def addentry(self, obj, c, path, subdirs):
if obj["location"] in self._pathmap:
commit bf43afc52fce505edbe3fad9daa6b0c729d02eeb
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 14:46:24 2016 -0400
9751: Bump cwltool dependency.
diff --git a/build/run-build-packages.sh b/build/run-build-packages.sh
index fec4950..8cb2330 100755
--- a/build/run-build-packages.sh
+++ b/build/run-build-packages.sh
@@ -467,7 +467,7 @@ fpm_build schema_salad "" "" python 1.14.20160708181155
fpm_build ruamel.yaml "" "" python 0.11.11 --python-setup-py-arguments "--single-version-externally-managed"
# And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
-fpm_build cwltool "" "" python 1.0.20160810161358
+fpm_build cwltool "" "" python 1.0.20160811184335
# FPM eats the trailing .0 in the python-rdflib-jsonld package when built with 'rdflib-jsonld>=0.3.0'. Force the version. Ward, 2016-03-25
fpm_build rdflib-jsonld "" "" python 0.3.0
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 35408b7..e22a74f 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160811170313',
+ 'cwltool==1.0.20160811184335',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
commit 6e0abcdabb14bcd21695420d3cfab0d57362a2be
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 14:19:37 2016 -0400
9751: Fix unit tests. Rename dir6.cwl to keep-dir-test-input.cwl
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index fd9e74f..f7792cd 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -114,6 +114,8 @@ class ArvCwlRunner(object):
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
self.pipeline = None
+ make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
+ self.fs_access = make_fs_access(kwargs["basedir"])
if kwargs.get("create_template"):
tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"))
@@ -124,8 +126,6 @@ class ArvCwlRunner(object):
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
- make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
- self.fs_access = make_fs_access(kwargs["basedir"])
kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 99237e1..35408b7 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160811124408',
+ 'cwltool==1.0.20160811170313',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 2526258..1187962 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -6,5 +6,5 @@
"class": "File",
"checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
}
- tool: dir6.cwl
+ tool: keep-dir-test-input.cwl
doc: Test directory in keep
diff --git a/sdk/cwl/tests/dir6.cwl b/sdk/cwl/tests/keep-dir-test-input.cwl
similarity index 100%
rename from sdk/cwl/tests/dir6.cwl
rename to sdk/cwl/tests/keep-dir-test-input.cwl
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 0d3a494..46d2048 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -3,6 +3,7 @@ import logging
import mock
import unittest
import os
+import functools
import cwltool.process
if not os.getenv('ARVADOS_DEBUG'):
@@ -28,7 +29,8 @@ class TestJob(unittest.TestCase):
}
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+ for j in arvtool.job({}, mock.MagicMock(), basedir="",
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)):
j.run()
runner.api.jobs().create.assert_called_with(
body={
commit 08698803d8b324ba9a889a3aa41559d782bcc4bf
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 13:01:41 2016 -0400
9751: Override realpath in CollectionFsAccess
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 0035597..9f11058 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -227,7 +227,7 @@ class RunnerJob(Runner):
logger.info("Submitted job %s", response["uuid"])
if kwargs.get("submit"):
- self.pipeline = self.arvrunner.api.pipeline_instances().create(
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
body={
"owner_uuid": self.arvrunner.project_uuid,
"name": shortname(self.tool.tool["id"]),
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 4b129cc..d258937 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -104,3 +104,12 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
return paths[-1]
return os.path.join(path, *paths)
+
+ def realpath(self, path):
+ if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
+ return path
+ collection, rest = self.get_collection(path)
+ if collection:
+ return path
+ else:
+ return os.path.realpath(path)
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 60ea7ab..99237e1 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160810161358',
+ 'cwltool==1.0.20160811124408',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
commit c961ea106e3528a2690f7ab1e0032fa68f650bfe
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Aug 10 13:45:56 2016 -0400
9751: Fix direct to keep directory references.
Add arvados-specific integration test for arvados-cwl-runner.
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 2a1873a..fe4e800 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -18,8 +18,9 @@ import logging
import os
import json
import argparse
+import re
from arvados.api import OrderedJsonModel
-from cwltool.process import adjustFileObjs
+from cwltool.process import adjustFileObjs, adjustDirObjs
from cwltool.load_tool import load_tool
# Print package versions
@@ -30,8 +31,10 @@ api = arvados.api("v1")
try:
job_order_object = arvados.current_job()['script_parameters']
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
+
def keeppath(v):
- if arvados.util.keep_locator_pattern.match(v):
+ if pdh_path.match(v):
return "keep:%s" % v
else:
return v
@@ -49,6 +52,7 @@ try:
}
adjustFileObjs(job_order_object, keeppathObj)
+ adjustDirObjs(job_order_object, keeppathObj)
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7bd9df3..fd9e74f 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -124,7 +124,9 @@ class ArvCwlRunner(object):
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
- self.fs_access = kwargs["make_fs_access"](kwargs["basedir"])
+ make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
+ self.fs_access = make_fs_access(kwargs["basedir"])
+ kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
kwargs["tmpdir_prefix"] = "tmp"
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 24c319c..7e9a159 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -52,7 +52,6 @@ class ArvPathMapper(PathMapper):
elif srcobj["class"] == "Directory":
if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
- else:
for l in srcobj["listing"]:
self.visit(l, uploadfiles)
diff --git a/sdk/cwl/tests/arvados-tests.sh b/sdk/cwl/tests/arvados-tests.sh
new file mode 100755
index 0000000..8646704
--- /dev/null
+++ b/sdk/cwl/tests/arvados-tests.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+if ! arv-get d7514270f356df848477718d58308cc4+94 > /dev/null ; then
+ arv-put --portable-data-hash testdir
+fi
+exec cwltest --test arvados-tests.yml --tool $PWD/runner.sh
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
new file mode 100644
index 0000000..2526258
--- /dev/null
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -0,0 +1,10 @@
+- job: dir-job.yml
+ output:
+ "outlist": {
+ "size": 20,
+ "location": "output.txt",
+ "class": "File",
+ "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
+ }
+ tool: dir6.cwl
+ doc: Test directory in keep
diff --git a/sdk/cwl/tests/dir-job.yml b/sdk/cwl/tests/dir-job.yml
new file mode 100644
index 0000000..91204d7
--- /dev/null
+++ b/sdk/cwl/tests/dir-job.yml
@@ -0,0 +1,3 @@
+indir:
+ class: Directory
+ location: keep:d7514270f356df848477718d58308cc4+94
\ No newline at end of file
diff --git a/sdk/cwl/tests/dir6.cwl b/sdk/cwl/tests/dir6.cwl
new file mode 100644
index 0000000..93362b5
--- /dev/null
+++ b/sdk/cwl/tests/dir6.cwl
@@ -0,0 +1,21 @@
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+ - class: ShellCommandRequirement
+inputs:
+ indir:
+ type: Directory
+ inputBinding:
+ prefix: cd
+ position: -1
+outputs:
+ outlist:
+ type: File
+ outputBinding:
+ glob: output.txt
+arguments: [
+ {shellQuote: false, valueFrom: "&&"},
+ "find", ".",
+ {shellQuote: false, valueFrom: "|"},
+ "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/sdk/cwl/tests/runner.sh b/sdk/cwl/tests/runner.sh
new file mode 100755
index 0000000..22ede5c
--- /dev/null
+++ b/sdk/cwl/tests/runner.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+exec arvados-cwl-runner --disable-reuse --compute-checksum "$@"
diff --git a/sdk/cwl/tests/testdir/a b/sdk/cwl/tests/testdir/a
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/testdir/b b/sdk/cwl/tests/testdir/b
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/testdir/c/d b/sdk/cwl/tests/testdir/c/d
new file mode 100644
index 0000000..e69de29
commit 46df7c2b292e5f12da365b918b0f28757eb4c4ce
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Aug 10 11:51:44 2016 -0400
9751: Provide make_fs_access=CollectionFsAccess and bump cwltool pin.
diff --git a/build/run-build-packages.sh b/build/run-build-packages.sh
index e1c0ac3..fec4950 100755
--- a/build/run-build-packages.sh
+++ b/build/run-build-packages.sh
@@ -467,7 +467,7 @@ fpm_build schema_salad "" "" python 1.14.20160708181155
fpm_build ruamel.yaml "" "" python 0.11.11 --python-setup-py-arguments "--single-version-externally-managed"
# And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
-fpm_build cwltool "" "" python 1.0.20160726135535
+fpm_build cwltool "" "" python 1.0.20160810161358
# FPM eats the trailing .0 in the python-rdflib-jsonld package when built with 'rdflib-jsonld>=0.3.0'. Force the version. Ward, 2016-03-25
fpm_build rdflib-jsonld "" "" python 0.3.0
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 99db9f1..7bd9df3 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -9,6 +9,7 @@ import os
import sys
import threading
import hashlib
+from functools import partial
import pkg_resources # part of setuptools
from cwltool.errors import WorkflowException
@@ -113,7 +114,6 @@ class ArvCwlRunner(object):
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
self.pipeline = None
- self.fs_access = CollectionFsAccess(kwargs["basedir"], api_client=self.api)
if kwargs.get("create_template"):
tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"))
@@ -124,7 +124,7 @@ class ArvCwlRunner(object):
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
- kwargs["fs_access"] = self.fs_access
+ self.fs_access = kwargs["make_fs_access"](kwargs["basedir"])
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
kwargs["tmpdir_prefix"] = "tmp"
@@ -341,4 +341,5 @@ def main(args, stdout, stderr, api_client=None):
executor=runner.arvExecutor,
makeTool=runner.arvMakeTool,
versionfunc=versionstring,
- job_order_object=job_order_object)
+ job_order_object=job_order_object,
+ make_fs_access=partial(CollectionFsAccess, api_client=api_client))
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index d2d38b0..4b129cc 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,14 +1,14 @@
import fnmatch
import os
-import cwltool.process
+import cwltool.stdfsaccess
from cwltool.pathmapper import abspath
import arvados.util
import arvados.collection
import arvados.arvfile
-class CollectionFsAccess(cwltool.process.StdFsAccess):
+class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
def __init__(self, basedir, api_client=None):
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 9fcbdd7..60ea7ab 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160726135535',
+ 'cwltool==1.0.20160810161358',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
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