July 2009 - galaxy-user - lists.galaxyproject.org

Fwd: Request for " Find cluster intervals" tool
by Anton Nekrutenko 22 Jul '09

22 Jul '09

Begin forwarded message: > From: "Charu Gupta Kumar" <cgkumar(a)illinois.edu> > Date: July 21, 2009 6:41:59 PM EDT > To: "'Anton Nekrutenko'" <anton(a)bx.psu.edu> > Subject: Request for " Find cluster intervals" tool > > Dear Dr. Nekrutenko, > > I was wondering if it would be possible to make a small change to > the "Find > cluster intervals, output grouped by clusters" tool (Find cluster > intervals; > output grouped by clusters is part of "Operate on Genomic Intervals"): > > Ques.) Would it be possible to add a newline (or ***) after every > cluster > grouping, so users know when one cluster starts and another ends? It > would > be most helpful in figuring out the cluster demarcations. > > Thanks so much, > > Best regards, > > Charu > Charu Gupta Kumar, Ph.D. > > ****************** > > For example, > > chr6_random 3253 3745 AA577868 0 + 3 > chr6_random 3663 3896 BI789243 0 + 1 > chr6_random 3663 4054 BM351966 0 + 1 > chr6_random 3663 7171 CK903338 0 + 3 > chr6_random 3847 7979 CK903339 0 - 4 > chr6_random 3878 7963 BI962749 0 - 4 > chr6_random 4062 7581 BM352279 0 - 4 > chr6_random 4610 5058 AA828152 0 + 2 > chr6_random 5243 5460 BM353279 0 - 2 > chr6_random 5255 5403 BM314916 0 + 1 > (space or ****** here) > chr6_random 23107 23724 BU657553 0 - 1 > chr6_random 23489 27653 BF507618 0 - 2 > chr6_random 27113 27791 BI086568 0 + 9 > chr6_random 70525 75802 BC064362 0 + 2 > chr6_random 70514 73863 DA960595 0 + 3 > chr6_random 70525 71258 BM470002 0 + 12 > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

1 0

Problems with history
by SHAUN WEBB 16 Jul '09

16 Jul '09

I have just updated galaxy with the latest mercurial change sets and I am having a few problems with the history. The history is not automatically refreshing so new jobs appear to still be queuing/running. Also, I can't permanently delete an item from the history. It remains with the message "This item has been deleted" even if I try to delete it again. Is this a feature in the latest update. Is anyone else having these problems? Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 3

library usage screencast?
by Erick Antezana 16 Jul '09

16 Jul '09

Hi, is there any screencast or documentation that could be used to learn more about the library usage? (from the users and admin points of view. In the case of the admin, I guess the user_library_import_dir and library_import_dir settings need only be changed?) thanks, Erick

3 6

Ultradeep sequencing analysis with Galaxy
by rocco.piazza 15 Jul '09

15 Jul '09

2 1

Galaxy user list
by Lisette Hörnblad 15 Jul '09

15 Jul '09

Hi, I'm not using Galaxy right now and I therefore would like to exit the user-list so that I don't get e-mails regarding Galaxy any more. Thank you very much! Best Regards Lisette

1 0

Re: [galaxy-user] RBAC and libraries
by Ido M. Tamir 15 Jul '09

15 Jul '09

On Tuesday 14 July 2009 17:42:16 Greg Von Kuster wrote: > Ido M. Tamir wrote: > > On Tuesday 14 July 2009 15:25:47 you wrote: > >> Hello Ido, > >> > All roles are required because of the complication of derived > permissions for datasets that are produced from running jobs on > different input datasets. Take, for example, two datasets, DatasetA, > and DatasetB. Access to DatasetA requires a user to be associated with > RoleA, and access to DatasetB with RoleB. It follows that DatasetAB ( > created by running a tool with DatasetA and DatasetB as inputs ) should > have both RoleA and RoleB associated for the access permission. > However, if ANY associated role was sufficient, this would allow users > who are only associated either RoleA OR RoleB to view data which was > originally not accessible to them. That is an important point. But if this is the best solution I am not sure yet - first I would like to get my data in, then I can think on the effects of combining them. Could you show me how I could solve the problem I presented in my previous e-mail without creating ad-hoc roles for every user combination? thank your very much, ido

2 2

Re: [galaxy-user] RBAC and libraries]
by Greg Von Kuster 14 Jul '09

14 Jul '09

Ido M. Tamir wrote: > On Tuesday 14 July 2009 15:25:47 you wrote: > >> Hello Ido, >> >> We're sorry to hear that you have encountered problems in working with >> dataset libraries and security in Galaxy. Please see my explanations >> below, and let me know if more clarification is needed or if you come >> across behavior that differs from that described. >> > > Unfortunately I am a bit slow and need more clarification. The behavior > does not differ from what you described and there I think lies my problem. > > >> 1) manage permissions: Role members can manage the roles associated with >> this dataset >> 2) access: Role members can import this dataset into their history for >> analysis. NOTE: Users must have every role associated with the access >> permission on this dataset in order to access it >> > > It is this NOTE that I don't understand. In every other case you allow one > of each role. In this case you require that it fits all of the roles. > All roles are required because of the complication of derived permissions for datasets that are produced from running jobs on different input datasets. Take, for example, two datasets, DatasetA, and DatasetB. Access to DatasetA requires a user to be associated with RoleA, and access to DatasetB with RoleB. It follows that DatasetAB ( created by running a tool with DatasetA and DatasetB as inputs ) should have both RoleA and RoleB associated for the access permission. However, if ANY associated role was sufficient, this would allow users who are only associated either RoleA OR RoleB to view data which was originally not accessible to them. > >> The "library dataset" permission "access" is a restrict permission. If >> no roles are associated with it, the library dataset is considered >> public, and all users can access it in the library. However, if a role >> is associated with the "access" permission on the library dataset, a >> user must have that role in order to access the dataset in the library. >> If more than 1 role is associated with the "access" permission, then >> a user must have all roles in order to access it. >> > But why do you model this permission like this - requiring all roles? > See above explanation > >>> You require that the user should have all of the roles that are currently >>> associated with the library. This makes simple things difficult and >>> complicated things impossible. >>> >> This is not necessarily the case - for example, user can have >> permission to add a library item, but not manage library permissions. >> What behavior are you seeing that leads you to this conclusion? >> > > I actually only talk about the "access" permission. Here the user has > to have all the roles associated with him (should have pointed this > out more). > > >> Do you mean user/group ( Galaxy has no concept that would differentiate >> a user from a bioinformatician )? It depends on how you set up your >> groups of users. You could have 1 group with all users, and associate >> that group with a role, then associate that role with each "library" >> permission. >> > But then as soon as I add a new user, that should not have access to the > datasets all the other users have, this policy scheme breaks down. > > Maybe I can explain what I intend in an example - and then you can > tell me how I should actually do this: > > users (I simplify and say no user is in more than one group): > userName group > user1 group1 > user2 group2 > user3 bioinfo > user4* group4 > > user4 is a collaborator of user1 - he should have access to the data > of user1 - not to the rest of group1 data. > > Dataset owner > A user1 > B user2 > > I would normally solve my policy problem by creating the following roles: > role members > r_u1 user1* > r_u2 user2* > r_u3 user3* > r_u4 user4* > r_g1 group1** > r_g2 group2** > r_g4 group4** > r_b user3 > > *I think galaxy automatically creates roles from users or allows association > of libraries with users, so this might not be necessary. > Galaxy automatically creates a "private" role for each user, but this is the only role that is automatically created. > **I think galaxy automatically adds the roles of the groups one is member of > to the users roles, so I don't add user1 to r_u1 etc... > > Then I would associate the following privileges with the datasets > Dataset modify access > A r_u1,r_b r_u1,r_g1,r_b,r_u4 > B r_u2,r_b r_u2,r_g2,r_b > > Galaxy does not allow me to grant these access privileges, because > there is no user having all the roles. > It would be very simple to solve, if you would model the access permission > like you model all the other permissions. > Hopefully my comments above clarify why this is necessary. The roles associated with the access permission on a dataset are "and", not "or". Otherwise data security quickly breaks down on datasets derived from others. I agree that it's tricky, but ensuring data is only accessible by the desired users was our highest priority in implementing RBAC. > > Thank you very much for you time, > ido > > > >

1 0

Standalone galaxy server and user management
by Andreas Kuntzagk 14 Jul '09

14 Jul '09

Hi, we want to use a standalone Galaxy server here and integrate that with our Sun Grinengine cluster. While I could find information on how to do that I also want to know if it's possible to use our local user database (NIS based) to manage the galaxy users and make their galaxy scripts running with their userid. Could somebody tell me if that is a) easy b) hard c) impossible regards, Andreas

3 6

Re: [galaxy-user] how to clear job queue?
by R 14 Jul '09

14 Jul '09

thanks for help! the error log as below: --------------------------------------------------------- galaxy.jobs.runners.local INFO 2009-07-13 17:30:21,924 starting workers galaxy.jobs.runners.local DEBUG 2009-07-13 17:30:21,945 5 workers ready galaxy.jobs.runners.local INFO 2009-07-13 17:30:21,950 starting workers galaxy.jobs.runners.local DEBUG 2009-07-13 17:30:21,969 5 workers ready galaxy.jobs.schedulingpolicy.roundrobin INFO 2009-07-13 17:30:21,992 RoundRobin policy: initialized galaxy.jobs INFO 2009-07-13 17:30:21,992 job scheduler policy is galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin galaxy.jobs INFO 2009-07-13 17:30:22,005 job manager started galaxy.jobs DEBUG 2009-07-13 17:30:22,202 no runner: 326 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-07-13 17:30:22,202 no runner: 330 is still in new state, adding to the jobs queue Traceback (most recent call last): File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/web/buildapp.py", line 56, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/app.py", line 66, in __init__ self.job_manager = jobs.JobManager( self ) File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/jobs/__init__.py", line 110, in __init__ self.__check_jobs_at_startup() File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/jobs/__init__.py", line 127, in __check_jobs_at_startup job_wrapper = JobWrapper( job, self.app.toolbox.tools_by_id[ job.tool_id ], self ) KeyError: u'xslt_converter_16' ---------------------------------------------------------- --- On Mon, 7/13/09, Nate Coraor <nate(a)bx.psu.edu> wrote: From: Nate Coraor <nate(a)bx.psu.edu> Subject: Re: [galaxy-user] how to clear job queue? To: "R" <riververy(a)yahoo.com> Cc: "galaxy" <galaxy-user(a)bx.psu.edu> Date: Monday, July 13, 2009, 9:36 AM R wrote: > I accidentally shut down my galaxy server in the middle of an job execution, after that I try to restart my galaxy server, it always shows the error that a job is in new state, and I can't start my galaxy server at all. I guess I have to clear that job out of the queue, so my galaxy server can start. > > Does anyone know how to clear the job queue? or any idea how to fix the problem? Hello, Can you provide us with any relevant terminal output or errors? Galaxy attempts to manage new/queued/running jobs upon startup and should not hang or crash during this process. --nate

2 1

how to clear the job queue
by R 14 Jul '09

14 Jul '09

I accidentally shut down my galaxy server in the middle of an job execution, after that I try to restart my galaxy server, it always shows the error that a job is in new state, and I can't start my galaxy server at all. I guess I have to clear that job out of the queue, so my galaxy server can start. Does anyone know how to clear the job queue? or any idea how to fix the problem? the error log as below: --------------------------------------------------------- galaxy.jobs.runners.local INFO 2009-07-13 17:30:21,924 starting workers galaxy.jobs.runners.local DEBUG 2009-07-13 17:30:21,945 5 workers ready galaxy.jobs.runners.local INFO 2009-07-13 17:30:21,950 starting workers galaxy.jobs.runners.local DEBUG 2009-07-13 17:30:21,969 5 workers ready galaxy.jobs.schedulingpolicy.roundrobin INFO 2009-07-13 17:30:21,992 RoundRobin policy: initialized galaxy.jobs INFO 2009-07-13 17:30:21,992 job scheduler policy is galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin galaxy.jobs INFO 2009-07-13 17:30:22,005 job manager started galaxy.jobs DEBUG 2009-07-13 17:30:22,202 no runner: 326 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2009-07-13 17:30:22,202 no runner: 330 is still in new state, adding to the jobs queue Traceback (most recent call last): File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/web/buildapp.py", line 56, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/app.py", line 66, in __init__ self.job_manager = jobs.JobManager( self ) File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/jobs/__init__.py", line 110, in __init__ self.__check_jobs_at_startup() File "/media/Applications/work/spring2009/galaxy/galaxy3/lib/galaxy/jobs/__init__.py", line 127, in __check_jobs_at_startup job_wrapper = JobWrapper( job, self.app.toolbox.tools_by_id[ job.tool_id ], self ) KeyError: u'xslt_converter_16'

1 0