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Native Docker + 16.04 #28

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Native Docker + 16.04 #28

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8 changes: 4 additions & 4 deletions dx-cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -518,7 +518,7 @@ def compile_tool_internal(tool, assets, bundled, folder='/', extradisk=10000, pr
runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
runSpec['distribution'] = "Ubuntu"
runSpec['release'] = "14.04"
runSpec['release'] = "16.04"
runSpec['assetDepends'] = []
runSpec['bundledDepends'] = []
if assets:
Expand Down Expand Up @@ -684,7 +684,7 @@ def compile_scatter_tool(workflow, sname, step, executable_id, folder='/', provi
runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
runSpec['distribution'] = "Ubuntu"
runSpec['release'] = "14.04"
runSpec['release'] = "16.04"
runSpec['assetDepends'] = []
runSpec['bundledDepends'] = []
if assets:
Expand Down Expand Up @@ -861,7 +861,7 @@ def shell_suppress(cmd, ignore_error=False):
runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
runSpec['distribution'] = "Ubuntu"
runSpec['release'] = "14.04"
runSpec['release'] = "16.04"
dxapp['runSpec'] = runSpec
dxapp['access'] = {"project": "CONTRIBUTE", "network": ["*"]}
with open(dirname+"/dxapp.json", "w") as f:
Expand Down Expand Up @@ -918,7 +918,7 @@ def compile_postprocess_tool(workflow, outputs, folder='/', provider='aws'):
runSpec['executionPolicy'] = { "restartOn": {"*": 1 } }
runSpec['timeoutPolicy'] = {"*": { "hours": 48 }}
runSpec['distribution'] = "Ubuntu"
runSpec['release'] = "14.04"
runSpec['release'] = "16.04"
dxapp['runSpec'] = runSpec
dxapp['access'] = {"project": "CONTRIBUTE", "network": ["*"]}
with open(dirname+"/dxapp.json", "w") as f:
Expand Down
5 changes: 1 addition & 4 deletions dx-cwl-applet-code.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,6 @@ def shell_suppress(cmd, ignore_error=False):
def main(**kwargs):
sh("apt-get update")
sh("apt-get install python-virtualenv samtools")
sh("git clone --recursive https://github.com/dnanexus/dx-toolkit.git")
sh("cd dx-toolkit && git checkout 0c818a5cce7164119e7a89d7415770e1ff2caece && cd ..")
sh("make -C dx-toolkit python dx-docker")
os.environ["PATH"] = "/home/dnanexus/dx-toolkit/bin"+":"+os.environ["PATH"]
os.environ["PYTHONPATH"] = "/home/dnanexus/dx-toolkit/share/dnanexus/lib/python2.7/site-packages:/home/dnanexus/dx-toolkit/lib64/python2.7/site-packages"+":"+os.environ["PYTHONPATH"]

Expand Down Expand Up @@ -117,7 +114,7 @@ def compile_input_generic(iname, ivalue):

print("Running CWL tool")
sh("mkdir -p cwloutputs")
sh("cwltool --leave-outputs --outdir cwloutputs --user-space-docker-cmd dx-docker tool.cwl cwlinputs.yml > cwl_job_outputs.json")
sh("cwltool --leave-outputs --outdir cwloutputs tool.cwl cwlinputs.yml > cwl_job_outputs.json")

print("Process CWL outputs")
output = {}
Expand Down