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
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 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 ___________________________________________________________ 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/
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
___________________________________________________________ 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:
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
___________________________________________________________ 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:
participants (2)
-
Jose Navas -
Nate Coraor