Working directory path with space and parentheses

[jason-weirather]

I have an similar issue to this https://github.com/broadinstitute/cromwell/issues/1306, but I don't think OP's solution fits whats going in my case since input files are not part of the issue.

Using the hello-world example:

task hello {
  String name

  command {
    echo 'Hello ${name}!'
  }
  output {
    File response = stdout()
  }
}

workflow test {
  call hello
}

with input

{
  "test.hello.name": "World"
}

I run $ cromwell run hello.wdl hello.json hello.out

I get the error message:

/Users/jasonweirather/Dropbox (Partners HealthCare)/projects/2017_08_FIRECLOUD/cromwell-executions/test/12ed39b6-cf8f-4ea1-a965-193cd89f99e9/call-hello/execution/stderr.background -bash: syntax error near unexpected token `('

Seems it may be having troubles being run from a working directory with a space and parentheses.

This was done on Mac OS X 10.12.6 in the bash terminal. Version of cromwell is cromwell: 28-5fd2237-SNAP

[mcovarr]

As a workaround you might want to do something like ln /Users/jasonweirather/Dropbox (Partners HealthCare) /Users/jasonweirather/Dropbox-PHC and run Cromwell out of the latter path.

[jason-weirather]

Thanks @mcovarr! ... I did something similar and it runs well. I just wanted to get the path handling on their radar 😄.

[mcovarr]

Great, glad you got past the problem. I agree Cromwell should be able to handle special characters in paths.

[jason-weirather]

@mcovarr Ran into this again. Not sure how a "User Requested Improvement" sits it in your planning, but I'd suggest this be considered as a bug, not a quality of life thing. I think proper path handling on supported operating systems should be standard, and hopefully not a big lift for a team like yours. Thanks!

[yfarjoun]

@mcovarr your workaround doesn't work for me (in osx). I'm in a linked directory, but the code will use the non-linked, i.e. with space, path...