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yuch7 / cwlexec

A new open source tool to run CWL workflows on LSF
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File literal not written to safe path #2

Open mr-c opened 6 years ago

mr-c commented 6 years ago 
Test [89/128] Test file literal as input

Test failed: /home/jenkins/cwlexec-0.1/cwlexec --outdir=/tmp/tmpgf1k1pyg --quiet v1.0/cat3-tool.cwl v1.0/file-literal.yml
Test file literal as input
Returned non-zero
Failed to write file "/common-workflow-language-master/v1.0/v1.0/file1-78a66506": /common-workflow-language-master/v1.0/v1.0/file1-78a66506 (Permission denied)

Here the user doesn't have permissions to write to /common-workflow-language-master/v1.0/v1.0/

liuboxa commented 6 years ago

cwlexec needs a working directory to run workflow, the working directory should be shared with a cluster, by default, the working directory is $HOME/cwl-workdir

For this case, cwlexec will create a temporary file in the working directory (/home/jenkins/cwl-workdir) to save the contents of the literal file, so we should make sure the cwlexec runner has the permission (read and write) to access the directory