How to install cwltool on windows

[Sergei Manakov]

Hi everyone,

I would appreciate any advice/suggestions regarding the easiest way to run cwltool on Windows 7 and 10. I tried following instructions on https://github.com/common-workflow-language/cwltool to install the official package from PyPi  (with pip install cwl-runner) with windows 10 and cygwin 2.3.0 (pip 8.1.1 from C:\Anaconda2\lib\site-packages (python 2.7)). The tool appeared to have been installed but on the first example job from http://www.commonwl.org/draft-3/UserGuide.html the tool produced and error:

 

cwl-runner 1st-tool.cwl echo-job.yml

Error reading file://C:\cygwin64\home\smanakov\CWL\1st-tool.cwl [Errno 22] invalid mode ('r') or filename: ''

I was able to install and run cwltool with pip install on CentOS, so I assume this issue is windows specific. Ideally it would be nice to be able to run cwltool in cygwin, but if there is a working containerized cwltool for MinGW + Docker, that could be good, too.

Thanks,
Sergei

[Michael Crusoe]

Thank you Sergei for your email,

The reference implementation of CWL currently targets Linux & OS X. I don't personally have a Microsoft Windows machine to develop on but I am happy to accept pull requests that add compatibility.

There may be CWL compliant implementations from others that have MS Windows compatibility, but I'm not aware of any.

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Michael R. Crusoe
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Common Workflow Language project
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[tanyalci...@gmail.com]

Dear Michael,

I had the same problem for Windows.I suspect that it has to do with the file path names where in Windows backslashes are used like C:\dir\testDir\... The problem is \t or some other characters will be taken as a tab character. So I think the path names might be better passed on as r'path to cwl file' so that they are interpreted as raw string. I was wondering if this would be a quick fix for you?

Regards,

On Monday, May 30, 2016 at 11:26:48 AM UTC+2, michael.crusoe wrote:

Thank you Sergei for your email,

The reference implementation of CWL currently targets Linux & OS X. I don't personally have a Microsoft Windows machine to develop on but I am happy to accept pull requests that add compatibility.

There may be CWL compliant implementations from others that have MS Windows compatibility, but I'm not aware of any.

On Mon, May 30, 2016 at 11:16 AM, Sergei Manakov <siarhei...@gmail.com> wrote:

Hi everyone,

I would appreciate any advice/suggestions regarding the easiest way to run cwltool on Windows 7 and 10. I tried following instructions on https://github.com/common-workflow-language/cwltool to install the official package from PyPi  (with pip install cwl-runner) with windows 10 and cygwin 2.3.0 (pip 8.1.1 from C:\Anaconda2\lib\site-packages (python 2.7)). The tool appeared to have been installed but on the first example job from http://www.commonwl.org/draft-3/UserGuide.html the tool produced and error:

 

cwl-runner 1st-tool.cwl echo-job.yml

Error reading file://C:\cygwin64\home\smanakov\CWL\1st-tool.cwl [Errno 22] invalid mode ('r') or filename: ''

I was able to install and run cwltool with pip install on CentOS, so I assume this issue is windows specific. Ideally it would be nice to be able to run cwltool in cygwin, but if there is a working containerized cwltool for MinGW + Docker, that could be good, too.

Thanks,
Sergei

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