ERROR: genrsa: Can't open "/etc/apache2/ssl/pass.key" for writing, Read-only file system

when I run the cwl tools on MAC, I gat an error message as following. Any suggestion?

genrsa: Can't open "/etc/apache2/ssl/pass.key" for writing, Read-only file system
[job bwa_index.cwl] Max memory used: 0MiB
[job bwa_index.cwl] Job error:
Error collecting output for parameter 'output':
bwa_index.cwl:30:5: Traceback (most recent call last):
bwa_index.cwl:30:5:
bwa_index.cwl:30:5:   File "/Users/yifanwang/Test/CWL_work/venv_cwl/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 612, in collect_output_ports
bwa_index.cwl:30:5:     compute_checksum=compute_checksum)
bwa_index.cwl:30:5:
bwa_index.cwl:30:5:   File "/Users/yifanwang/Test/CWL_work/venv_cwl/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 692, in collect_output
bwa_index.cwl:30:5:     raise
bwa_index.cwl:30:5:
bwa_index.cwl:30:5:   File "/Users/yifanwang/Test/CWL_work/venv_cwl/lib/python2.7/site-packages/schema_salad/sourceline.py", line 166, in __exit__
bwa_index.cwl:30:5:     raise self.makeError("\n".join(traceback.format_exception(exc_type, exc_value, tb)))
bwa_index.cwl:30:5:
WorkflowException: bwa_index.cwl:33:7: Traceback (most recent call last):
bwa_index.cwl:33:7:
bwa_index.cwl:33:7:   File "/Users/yifanwang/Test/CWL_work/venv_cwl/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 664, in collect_output
bwa_index.cwl:33:7:     if gb.startswith(outdir):
bwa_index.cwl:33:7:
bwa_index.cwl:33:7: AttributeError: 'CommentedMap' object has no attribute 'startswith'
[job bwa_index.cwl] completed permanentFail
[job bwa_index.cwl] {}
[job bwa_index.cwl] Removing input staging directory /var/folders/1m/zpv1ttyd3klg2ywkv8c_r4z40000gn/T/dVzS1t
[job bwa_index.cwl] Removing temporary directory /var/folders/1m/zpv1ttyd3klg2ywkv8c_r4z40000gn/T/BcLAm1
{}
Final process status is permanentFail

[jpellman]

That looks like an issue with Docker. In particular this line is being executed and failing within the container. Not sure what’s happening exactly, but this might point you in the right direction.

[ttubb]

Looks like i’m late to the party. I got the tool running by using another container aus mr-c suggested. One hint: You have to change

    outputBinding:
      glob: $(inputs.reference)

to

    outputBinding:
      glob: $(inputs.reference.basename)

to make the output collection work.