Hi Nate, I'm using the output dataset path to generate an html file and in the output dataset's files_path/extra_files_path attribute I'm generating a set of files and directories. So the problem was in the output dataset's files_path/extra_files_path attribute. Thanks,Jose

Subject: Re: [galaxy-dev] Error copying files from job_working_directory From: nate@bx.psu.edu Date: Thu, 19 Apr 2012 12:16:05 -0400 CC: galaxy-dev@lists.bx.psu.edu To: josenavasmolina@hotmail.com

On Apr 16, 2012, at 9:03 PM, Jose Navas wrote:

...

Hi everybody,

I was searching through the Galaxy code and I find the solution: the function responsible for copying files is using shutil.copy function, which only allows copy files. I've modified this function to use shutil.copytree in case of file_name is a directory. I can send you the code if you email me.

Also, I don't know if there is a good reason against this solution. If it is, I will be very grateful if somebody can explain it.

Thanks,

Jose

Hi Jose,

Are you using the output dataset path as a directory rather than a filename? Or is this with the output dataset's files_path/extra_files_path attribute?

--nate

...

From: josenavasmolina@hotmail.com To: galaxy-dev@lists.bx.psu.edu Date: Mon, 16 Apr 2012 17:34:29 +0000 Subject: [galaxy-dev] Error copying files from job_working_directory

Hello,

I've integrated a tool into my Galaxy instance, but when I run the tool I get this error:

galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying /home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous to /home/galaxy/galaxy-dist/database/files/000/dataset_431_files/unweighted_unifrac_2d_continuous: [Errno 21] Is a directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous'

As I can see, it fails because it is trying to copy a directory. Is this feature supported in Galaxy? If it is supported, what I have to do to enable copy the directories from the job_working_directory?

Thank you,

Jose

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