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 <o...@hpc.ufl.edu> wrote: > > On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk <andreas.kuntz...@mdc-berlin.de> > 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/
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___________________________________________________________ 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/