Re: [galaxy-dev] Permission denied error for velveth
Was velveth working prior to the patch (i.e. is it okay to use extra_files_path on outputs?) or does some more work need to be done at the infrastructure level to copy output extra files over in run-as-user mode? -John On Thu, Dec 6, 2012 at 4:52 AM, Andreas Kuntzagk wrote: > Ok, > > while velveth seems to work now, if I put the result into velvetg I get > another error: > > Traceback (most recent call last): > File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line > 175, in queue_job > job_wrapper.prepare() > File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 184, in > prepare > self.command_line = self.tool.build_command_line( param_dict ) > File "/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2424, > in build_command_line > command_line = fill_template( self.command, context=param_dict ) > File "/data/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in > fill_template > return str( Template( source=template_text, searchList=[context] ) ) > File > "/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", > line 1004, in __str__ > return getattr(self, mainMethName)() > File "cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py", > line 84, in respond > NotFound: cannot find 'files_path' while searching for 'input.files_path' > > Andreas > > > On 06.12.2012 10:52, Andreas Kuntzagk wrote: >> >> Sorry, I think I had not really restarted galaxy after making the change. >> After I changed some logging options in universe_wsgi.ini and restarted >> it's suddenly working. >> So I can confirm your fix works. >> >> Thank you for your help. >> >> Andreas >> >> On 05.12.2012 13:40, Andreas Kuntzagk wrote: >>> >>> Hi, >>> >>> Does not work for me. I still get the same error. >>> If you need me to run more test, just email me. >>> >>> regards, Andreas >>> >>> On 04.12.2012 18:27, John Chilton wrote: I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached patch or has something like this been tried and there is some other problem? -John (09:43:01 AM) jmchilton: Is the velvet problem related to something specific about how velvet runs or do no tools that depend on extra_files_path work with as-user jobs? (10:10:31 AM) natefoo: they have to either write to files_path or extra_files_path, let me find the email... (10:12:24 AM) natefoo: http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219 (10:12:26 AM) mrscribe: Title: Galaxy Development List Archive - Folder permissions after cluster run (at dev.list.galaxyproject.org) (11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as changing extra_files_path to files_path in the wrappers then? On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko wrote: > > > On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk > wrote: > >> I see that this issue came up before by Oleksandr Moskalenko in >> October but was unresolved then. >> Is there a workaround now? >> >> regards, Andreas > > > The velvet wrapper is not going to be usable for real user jobs until > someone rewrites it to work > without direct manipulation of files in the database/ tree. No work has > been done on this nor any > is planned as far as I know. > > Regards, > > Alex > ___ > 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/ >>> >>> >> > > -- > Andreas Kuntzagk > > SystemAdministrator > > Berlin Institute for Medical Systems Biology at the > Max-Delbrueck-Center for Molecular Medicine > Robert-Roessle-Str. 10, 13125 Berlin, Germany > > http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich > ___ > 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/
Re: [galaxy-dev] Permission denied error for velveth
Ok, while velveth seems to work now, if I put the result into velvetg I get another error: Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 175, in queue_job job_wrapper.prepare() File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 184, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2424, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/data/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py", line 84, in respond NotFound: cannot find 'files_path' while searching for 'input.files_path' Andreas On 06.12.2012 10:52, Andreas Kuntzagk wrote: Sorry, I think I had not really restarted galaxy after making the change. After I changed some logging options in universe_wsgi.ini and restarted it's suddenly working. So I can confirm your fix works. Thank you for your help. Andreas On 05.12.2012 13:40, Andreas Kuntzagk wrote: Hi, Does not work for me. I still get the same error. If you need me to run more test, just email me. regards, Andreas On 04.12.2012 18:27, John Chilton wrote: I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached patch or has something like this been tried and there is some other problem? -John (09:43:01 AM) jmchilton: Is the velvet problem related to something specific about how velvet runs or do no tools that depend on extra_files_path work with as-user jobs? (10:10:31 AM) natefoo: they have to either write to files_path or extra_files_path, let me find the email... (10:12:24 AM) natefoo: http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219 (10:12:26 AM) mrscribe: Title: Galaxy Development List Archive - Folder permissions after cluster run (at dev.list.galaxyproject.org) (11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as changing extra_files_path to files_path in the wrappers then? On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko wrote: On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk wrote: I see that this issue came up before by Oleksandr Moskalenko in October but was unresolved then. Is there a workaround now? regards, Andreas The velvet wrapper is not going to be usable for real user jobs until someone rewrites it to work without direct manipulation of files in the database/ tree. No work has been done on this nor any is planned as far as I know. Regards, Alex ___ 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/ -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
Re: [galaxy-dev] Permission denied error for velveth
Sorry, I think I had not really restarted galaxy after making the change. After I changed some logging options in universe_wsgi.ini and restarted it's suddenly working. So I can confirm your fix works. Thank you for your help. Andreas On 05.12.2012 13:40, Andreas Kuntzagk wrote: Hi, Does not work for me. I still get the same error. If you need me to run more test, just email me. regards, Andreas On 04.12.2012 18:27, John Chilton wrote: I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached patch or has something like this been tried and there is some other problem? -John (09:43:01 AM) jmchilton: Is the velvet problem related to something specific about how velvet runs or do no tools that depend on extra_files_path work with as-user jobs? (10:10:31 AM) natefoo: they have to either write to files_path or extra_files_path, let me find the email... (10:12:24 AM) natefoo: http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219 (10:12:26 AM) mrscribe: Title: Galaxy Development List Archive - Folder permissions after cluster run (at dev.list.galaxyproject.org) (11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as changing extra_files_path to files_path in the wrappers then? On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko wrote: On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk wrote: I see that this issue came up before by Oleksandr Moskalenko in October but was unresolved then. Is there a workaround now? regards, Andreas The velvet wrapper is not going to be usable for real user jobs until someone rewrites it to work without direct manipulation of files in the database/ tree. No work has been done on this nor any is planned as far as I know. Regards, Alex ___ 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/ -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
Re: [galaxy-dev] Permission denied error for velveth
Hi, Does not work for me. I still get the same error. If you need me to run more test, just email me. regards, Andreas On 04.12.2012 18:27, John Chilton wrote: I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached patch or has something like this been tried and there is some other problem? -John (09:43:01 AM) jmchilton: Is the velvet problem related to something specific about how velvet runs or do no tools that depend on extra_files_path work with as-user jobs? (10:10:31 AM) natefoo: they have to either write to files_path or extra_files_path, let me find the email... (10:12:24 AM) natefoo: http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219 (10:12:26 AM) mrscribe: Title: Galaxy Development List Archive - Folder permissions after cluster run (at dev.list.galaxyproject.org) (11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as changing extra_files_path to files_path in the wrappers then? On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko wrote: On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk wrote: I see that this issue came up before by Oleksandr Moskalenko in October but was unresolved then. Is there a workaround now? regards, Andreas The velvet wrapper is not going to be usable for real user jobs until someone rewrites it to work without direct manipulation of files in the database/ tree. No work has been done on this nor any is planned as far as I know. Regards, Alex ___ 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/ -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
Re: [galaxy-dev] Permission denied error for velveth
I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached patch or has something like this been tried and there is some other problem? -John (09:43:01 AM) jmchilton: Is the velvet problem related to something specific about how velvet runs or do no tools that depend on extra_files_path work with as-user jobs? (10:10:31 AM) natefoo: they have to either write to files_path or extra_files_path, let me find the email... (10:12:24 AM) natefoo: http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219 (10:12:26 AM) mrscribe: Title: Galaxy Development List Archive - Folder permissions after cluster run (at dev.list.galaxyproject.org) (11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as changing extra_files_path to files_path in the wrappers then? On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko wrote: > > On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk > wrote: > >> I see that this issue came up before by Oleksandr Moskalenko in October but >> was unresolved then. >> Is there a workaround now? >> >> regards, Andreas > > The velvet wrapper is not going to be usable for real user jobs until someone > rewrites it to work without direct manipulation of files in the database/ > tree. No work has been done on this nor any is planned as far as I know. > > Regards, > > Alex > ___ > 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/ velvet.patch Description: Binary data ___ 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/
Re: [galaxy-dev] Permission denied error for velveth
On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk wrote: > I see that this issue came up before by Oleksandr Moskalenko in October but > was unresolved then. > Is there a workaround now? > > regards, Andreas The velvet wrapper is not going to be usable for real user jobs until someone rewrites it to work without direct manipulation of files in the database/ tree. No work has been done on this nor any is planned as far as I know. Regards, Alex ___ 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/
Re: [galaxy-dev] Permission denied error for velveth
I see that this issue came up before by Oleksandr Moskalenko in October but was unresolved then. Is there a workaround now? regards, Andreas On 29.11.2012 11:47, Andreas Kuntzagk wrote: Hi, I enabled velvet on our local install. But when I try to use velveth, I get an "Permission denied: '/data/galaxy/galaxy-dist/database/files/027/dataset_27903_files'" This file does not exist. Only file there is /data/galaxy/galaxy-dist/database/files/027/dataset_27903_dat regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
[galaxy-dev] Permission denied error for velveth
Hi, I enabled velvet on our local install. But when I try to use velveth, I get an "Permission denied: '/data/galaxy/galaxy-dist/database/files/027/dataset_27903_files'" This file does not exist. Only file there is /data/galaxy/galaxy-dist/database/files/027/dataset_27903_dat regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
