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When invoked with --tmpdir-prefix /vol/sge-tmp (a directory), cwltool doesn't add a trailing slash, and workflow
execution fails:
ERROR Unexpected exception
Traceback (most recent call last):
File "/vol/mgx-sw/lib/venvs/cwltool/lib/python3.11/site-packages/cwltool/workflow.py", line 459, in job
yield from self.embedded_tool.job(
File "/vol/mgx-sw/lib/venvs/cwltool/lib/python3.11/site-packages/cwltool/command_line_tool.py", line 960, in job
builder = self._init_job(job_order, runtimeContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/vol/mgx-sw/lib/venvs/cwltool/lib/python3.11/site-packages/cwltool/process.py", line 857, in _init_job
tmpdir = fs_access.realpath(runtime_context.get_tmpdir())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/vol/mgx-sw/lib/venvs/cwltool/lib/python3.11/site-packages/cwltool/context.py", line 215, in get_tmpdir
return self.create_tmpdir()
^^^^^^^^^^^^^^^^^^^^
File "/vol/mgx-sw/lib/venvs/cwltool/lib/python3.11/site-packages/cwltool/context.py", line 227, in create_tmpdir
return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/vol/mgx-sw/lib/python3.11/tempfile.py", line 368, in mkdtemp
_os.mkdir(file, 0o700)
PermissionError: [Errno 13] Permission denied: '/vol/sge-tmpv4nl9n8x'
ERROR Cannot make scatter job: [Errno 13] Permission denied: '/vol/sge-tmpv4nl9n8x'
I just discussed this with @mr-c, and he suggested to provide a better error message to create_tmpdir() in cwltool.context,
i.e. suggesting to either adding a trailing slash to the argument or to check for write permissions.
The text was updated successfully, but these errors were encountered:
When invoked with
--tmpdir-prefix /vol/sge-tmp
(a directory), cwltool doesn't add a trailing slash, and workflowexecution fails:
I just discussed this with @mr-c, and he suggested to provide a better error message to
create_tmpdir()
incwltool.context
,i.e. suggesting to either adding a trailing slash to the argument or to check for write permissions.
The text was updated successfully, but these errors were encountered: