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: n...@bx.psu.edu > Date: Thu, 19 Apr 2012 12:16:05 -0400 > CC: galaxy-dev@lists.bx.psu.edu > To: josenavasmol...@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: josenavasmol...@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 > > > > ___________________________________________________________ Please keep all > > replies on the list by using "reply all" in your mail client. To manage > > your subscriptions to this and other Galaxy lists, please use the interface > > at:http://lists.bx.psu.edu/ > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ >
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