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/ ___________________________________________________________ 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/
