renku run Rscript src/simulate.R outputs/simdata.csv
renku run Rscript src/plot.R --input outputs/simdata.csv --output outputs/plot.pdf
renku run Rscript src/estimate.R --input outputs/simdata.csv --output outputs/estimate.Rout
Traceback (most recent call last):
File "[...]/renku/cli/_exc.py", line 100, in main
result = super().main(*args, **kwargs)
File "[...]/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "[...]/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "[...]/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "[...]/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "[...]/renku/cli/_client.py", line 83, in new_func
result = ctx.invoke(method, client, *args, **kwargs)
File "[...]/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "[...]/renku/cli/update.py", line 194, in update
execute(client, output_file, output_paths=output_paths)
File "[...]/renku/cli/_cwl.py", line 70, in execute
process = factory.make(os.path.relpath(str(output_file)))
File "[...]/cwltool/factory.py", line 58, in make
load = load_tool.load_tool(cwl, self.loading_context)
File "[...]/cwltool/load_tool.py", line 378, in load_tool
loadingContext)
File "[...]/cwltool/load_tool.py", line 346, in make_tool
tool = loadingContext.construct_tool_object(processobj, loadingContext)
File "[...]/renku/cli/_cwl.py", line 47, in construct_tool_object
return workflow.default_make_tool(toolpath_object, *args, **kwargs)
File "[...]/cwltool/workflow.py", line 54, in default_make_tool
return Workflow(toolpath_object, loadingContext)
File "[...]/cwltool/workflow.py", line 531, in __init__
loadingContext.prov_obj))
File "[...]/cwltool/workflow.py", line 619, in __init__
toolpath_object["run"], loadingContext)
File "[...]/cwltool/load_tool.py", line 378, in load_tool
loadingContext)
File "[...]/cwltool/load_tool.py", line 346, in make_tool
tool = loadingContext.construct_tool_object(processobj, loadingContext)
File "[...]/renku/cli/_cwl.py", line 47, in construct_tool_object
return workflow.default_make_tool(toolpath_object, *args, **kwargs)
File "[...]/cwltool/workflow.py", line 50, in default_make_tool
return command_line_tool.CommandLineTool(toolpath_object, loadingContext)
File "[...]/cwltool/command_line_tool.py", line 229, in __init__
super(CommandLineTool, self).__init__(toolpath_object, loadingContext)
File "[...]/cwltool/process.py", line 595, in __init__
validate_js_expressions(cast(CommentedMap, toolpath_object), self.doc_schema.names[toolpath_object["class"]], validate_js_options)
File "[...]/cwltool/validate_js.py", line 193, in validate_js_expressions
expression_errors, _ = jshint_js(code_fragment_js, js_globals, jshint_options)
File "[...]/cwltool/validate_js.py", line 118, in jshint_js
context=jshint_functions_text
File "[...]/cwltool/sandboxjs.py", line 161, in exec_js_process
new_proc = new_js_proc(js_engine_code, force_docker_pull=force_docker_pull)
File "[...]/cwltool/sandboxjs.py", line 110, in new_js_proc
u"docker run node:slim".format(u", ".join(trynodes)))
cwltool.sandboxjs.JavascriptException: cwltool requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim
Describe the bug
Trying to
run renkuupdate after editingoutputs/simdata.csv.The KG display looks intriguing:
I ran the commands 3 times and I see:
https://renkulab.io/projects/1383/files/lineage/src/estimate.R
Is it for all the renku runs? Because there's actually only one file:
Details
Renku version: 0.5.2
OS: Linux (#1 SMP Mon Oct 22 10:40:32 EDT 2018)
Python: 3.7.4
Traceback