Re: [galaxy-dev] Error when adding datasets
On 04/14/2011 07:36 PM, Greg Von Kuster wrote: Hello Louise, I've CC'd Nate on this as he may be able to help - although no guarantees. I'm not expert enough in this area to know where to look for the cause. Perhaps someone in the community can help as well. It is likely that LDAP is playing a role in this behavior. Hi I am sure you have tested everything, but just to double check - is your PostgreSQL database in sync with the database folder? - are you sure there is no second galaxy installation accessing the same PostgreSQL database? - you mention, that you have started with an empty PostgreSQL database, so this last question does probably not apply: make sure you have the right user names (you even run into trouble with case sensitivity) in your PostgreSQL database. We had troubles when we switched to external authentication: some users just couldn't work anymore, ie could not create new history items anymore. The problem was then solved by fixing their user names in the (MySQL) database. Regards, Hans On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote: The thing is, we use LDAP logging so we can't even access the website without logging in. Moreover, when I logged in, I arrived on the data analysis page where the automatic unnamed history was obviously created in the history panel. I forgot to mention we have issues creating and deleting histories, like, we can't access some histories and everytime we delete histories, two extra unnamed histories are created. As I mentioned before, it is also impossible to load a dataset in any history, existing or not. Do you think it could be linked to our using LDAP? Thanks L-A On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kusterg...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you. galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans:galaxy.web.framework.GalaxyWebUITransaction object at 0x29f40950 galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans.sa_session:sqlalchemy.orm.scoping.ScopedSession object at 0x19ab21d0 Thanks again L-A Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and reply back with the output of the debug statements. Assuming you start your Galaxy instance with: sh run.sh you'll see the results of the debug statements in the log scrolling in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think this issue is related to the Galaxy eggs, but instead looks like a data issue of some kind. Please replly back with answers to the following questions. How did you create your database? Couldn't have done it more simply ^^: CREATE DATABASE galaxy_db; GRANT ALL ON DATABASE galaxy_db TO galaxy; executed in psql. The very same way I did for the one that's still working fine. Did you populate it with any data exported from another database? In the beginning yes but when I saw that error I dropped the database and
Re: [galaxy-dev] Error when adding datasets
On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote: Hi Hans, thanks for your reply. - is your PostgreSQL database in sync with the database folder? I'm sorry I'm not sure I get what you mean, what folder is it? the folder where you keep the datasets, eg: your local path/galaxy_dist/database/ and it particular your local path/galaxy_dist/database/files/000/dataset_*.dat if you have an empty PostgreSQL database, then there should also be no datasets. Hans - are you sure there is no second galaxy installation accessing the same PostgreSQL database? Never been this sure of something before. :) I installed both galaxy and postgresql myself so I can guarantee there's ony one galaxy install on it. - you mention, that you have started with an empty PostgreSQL database, so this last question does probably not apply: make sure you have the right user names (you even run into trouble with case sensitivity) in your PostgreSQL database. We had troubles when we switched to external authentication: some users just couldn't work anymore, ie could not create new history items anymore. The problem was then solved by fixing their user names in the (MySQL) database. Yes, the username is properly created in the database when I log in on an empty database. We never used anything besides LDAP anyway. Regards, Hans Cheers, L-A On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote: The thing is, we use LDAP logging so we can't even access the website without logging in. Moreover, when I logged in, I arrived on the data analysis page where the automatic unnamed history was obviously created in the history panel. I forgot to mention we have issues creating and deleting histories, like, we can't access some histories and everytime we delete histories, two extra unnamed histories are created. As I mentioned before, it is also impossible to load a dataset in any history, existing or not. Do you think it could be linked to our using LDAP? Thanks L-A On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kusterg...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you. galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans:galaxy.web.framework.GalaxyWebUITransaction object at 0x29f40950 galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans.sa_session:sqlalchemy.orm.scoping.ScopedSession object at 0x19ab21d0 Thanks again L-A Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and reply back with the output of the debug statements. Assuming you start your Galaxy instance with: sh run.sh you'll see the results of the debug statements in the log scrolling in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think this issue is related to the Galaxy eggs, but instead looks like a data issue of some kind. Please replly back with answers to the following questions. How did you
[galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets
Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro ___ 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] Error in user registration
Hello, it seems since I updated to the newest galaxy-dist, I always get an error when trying to register a new user. When I try it from the admin panel, the error is the following: Error - type 'exceptions.NameError': Undefined URL: http://solweb2.immunbio.mpg.de/user/create?cntrller=adminwebapp=galaxy File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/user.py', line 523 in create status=status ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 69 in render_body __M_writer(unicode(render_registration_form())) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 40 in render_registration_form return render_render_registration_form(context.locals_(__M_locals),form_action) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 121 in render_render_registration_form form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 248 in url_for url = config.mapper.generate(*route_args, **newargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/mapper.py', line 823 in generate path = route.generate(**kargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/route.py', line 736 in generate fragments.append((key, _str_encode(val, self.encoding))) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 129 in _str_encode s = unicode(string).encode(encoding) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 128 in __str__ raise NameError(Undefined) NameError: Undefined If I log out and try it from the User menu, I get the following error: Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/create File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: create() takes at least 3 arguments (2 given) I have no idea what is going on, any help is greatly appreciated, thank you! Best regards, Sarah Diehl ___ 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] Error in user registration
Hello Sarah, The method signature for the user controller's index method changed in the latest distribution update, and your browser cache is causing the problem because it is using the old method signature. Refreshing the masthead in your browser should solve the problem. By masthead, I mean the following - right click on it and select Reload page, or whatever your browser provides for an option: inline: masthead.tiff On Apr 15, 2011, at 8:31 AM, Sarah Diehl wrote: Hello, it seems since I updated to the newest galaxy-dist, I always get an error when trying to register a new user. When I try it from the admin panel, the error is the following: Error - type 'exceptions.NameError': Undefined URL: http://solweb2.immunbio.mpg.de/user/create?cntrller=adminwebapp=galaxy File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/user.py', line 523 in create status=status ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 69 in render_body __M_writer(unicode(render_registration_form())) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 40 in render_registration_form return render_render_registration_form(context.locals_(__M_locals),form_action) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 121 in render_render_registration_form form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 248 in url_for url = config.mapper.generate(*route_args, **newargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/mapper.py', line 823 in generate path = route.generate(**kargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/route.py', line 736 in generate fragments.append((key, _str_encode(val, self.encoding))) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 129 in _str_encode s = unicode(string).encode(encoding) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 128 in __str__ raise NameError(Undefined) NameError: Undefined If I log out and try it from the User menu, I get the following error: Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/create File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: create() takes at least 3 arguments (2 given) I have no idea what is going on, any help is greatly appreciated,
Re: [galaxy-dev] Error in user registration
Hello Greg, first thank you for your help. I tried reloading everything, cleared the cache of my browser and tried it on a different computer whose browser never before was on the Galaxy website. All of this did not work. What worked in the end was deleting the compiled_templates directory. Best regards, Sarah On 04/15/2011 03:14 PM, Greg Von Kuster wrote: Hello Sarah, The method signature for the user controller's index method changed in the latest distribution update, and your browser cache is causing the problem because it is using the old method signature. Refreshing the masthead in your browser should solve the problem. By masthead, I mean the following - right click on it and select Reload page, or whatever your browser provides for an option: On Apr 15, 2011, at 8:31 AM, Sarah Diehl wrote: Hello, it seems since I updated to the newest galaxy-dist, I always get an error when trying to register a new user. When I try it from the admin panel, the error is the following: Error -type 'exceptions.NameError': Undefined URL: http://solweb2.immunbio.mpg.de/user/create?cntrller=adminwebapp=galaxy File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/user.py', line 523 in create status=status ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 inlambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 69 in render_body __M_writer(unicode(render_registration_form())) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 40 in render_registration_form return render_render_registration_form(context.locals_(__M_locals),form_action) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 121 in render_render_registration_form form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 248 in url_for url = config.mapper.generate(*route_args, **newargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/mapper.py', line 823 in generate path = route.generate(**kargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/route.py', line 736 in generate fragments.append((key, _str_encode(val, self.encoding))) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 129 in _str_encode s = unicode(string).encode(encoding) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 128 in __str__ raise NameError(Undefined) NameError: Undefined If I log out and try it from the User menu, I get the following error: Error -type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/create File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ,
Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets
I've essentially asked the same question of the list in the past and gotten no real response. I have the same interest, but from a workflow perspective. * A module that allows me to select multiple datafiles (say fastq files) * Then pass each data file to a separate instance of a workflow that runs tophat and cufflinks * then another module that takes the final outputs of each of the workflow runs and sends them to a final module that merges results. I am attempting to implement something like this using the API, though the API is still pretty green from my perspective. I think functionality like this built into the workflow editor would be a great addition. Dave On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote: Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro ATT1..txt ___ 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] Launching multiple jobs using one tool form with multiple selected datasets
Hi Our production pipeline does this on LSF through job arrays. It would be good if Galaxy supported job arrays Marina On 15/04/2011 13:14, Leandro Hermida wrote: Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro ___ 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/ -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___ 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] Error when adding datasets
Ooops, this is very right, I totally forgot about that. It woud have become problematic at some point I guess. Thank you for pointing this out! I changed it so the new database is associated with brand new appropriate directories. (and dropped and re-created the db again) But I keep getting the same error message with supposedly nonexistent histories. Thanks again L-A Le vendredi 15 avril 2011 à 13:47 +0200, Hans-Rudolf Hotz a écrit : On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote: Hi Hans, thanks for your reply. - is your PostgreSQL database in sync with the database folder? I'm sorry I'm not sure I get what you mean, what folder is it? the folder where you keep the datasets, eg: your local path/galaxy_dist/database/ and it particular your local path/galaxy_dist/database/files/000/dataset_*.dat if you have an empty PostgreSQL database, then there should also be no datasets. Hans - are you sure there is no second galaxy installation accessing the same PostgreSQL database? Never been this sure of something before. :) I installed both galaxy and postgresql myself so I can guarantee there's ony one galaxy install on it. - you mention, that you have started with an empty PostgreSQL database, so this last question does probably not apply: make sure you have the right user names (you even run into trouble with case sensitivity) in your PostgreSQL database. We had troubles when we switched to external authentication: some users just couldn't work anymore, ie could not create new history items anymore. The problem was then solved by fixing their user names in the (MySQL) database. Yes, the username is properly created in the database when I log in on an empty database. We never used anything besides LDAP anyway. Regards, Hans Cheers, L-A On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote: The thing is, we use LDAP logging so we can't even access the website without logging in. Moreover, when I logged in, I arrived on the data analysis page where the automatic unnamed history was obviously created in the history panel. I forgot to mention we have issues creating and deleting histories, like, we can't access some histories and everytime we delete histories, two extra unnamed histories are created. As I mentioned before, it is also impossible to load a dataset in any history, existing or not. Do you think it could be linked to our using LDAP? Thanks L-A On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kusterg...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you. galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans:galaxy.web.framework.GalaxyWebUITransaction object at 0x29f40950 galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans.sa_session:sqlalchemy.orm.scoping.ScopedSession object at 0x19ab21d0 Thanks again L-A Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and
Re: [galaxy-dev] uploading a large number of files to a library
On Apr 15, 2011, at 7:15 AM, Glen Beane wrote: I have been having trouble uploading a large number of fastq files to a library (180). I am uploading a directory of files, and I am not copying the files into Galaxy. When I try to view the files in the library after uploading it takes a long time to load the library view (sometimes it times out), and when it does load it lists every file three times so instead of there being 180 fastq files in the library there are 540. I have tried this multiple times after deleting the library and starting over, and each time it looks like there are three copies of each file. Has anyone else had trouble uploading a large number of fastq files into a library at the same time? I tried to delete a bunch of the duplicate files but it just timed out. I ended up creating 6 libraries, and split the files between these with no problems. It seems there is a problem when uploading a large number of files into a single library. I could open the library maybe one time out of 6, the rest it would time out, and when it did open each file showed up three times. After I split between 6 different libraries they open almost instantly and each file shows up once. I am running the last dist release, not the most recent one. -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___ 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/ -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___ 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] uploading a large number of files to a library
Hello Glen, I advise upgrading to the latest dist release - it includes performance improvements for displaying data libraries that contain many folders / library datasets. The change set that helps this issue disabled problematic eager loading on data libraries. Very large data libraries will load two to three times quicker. See our news brief at https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08 for details. Perhaps you've discovered a different problem, but upgrading will at least eliminate some known issues. Greg Von Kuster On Apr 15, 2011, at 10:54 AM, Glen Beane wrote: On Apr 15, 2011, at 7:15 AM, Glen Beane wrote: I have been having trouble uploading a large number of fastq files to a library (180). I am uploading a directory of files, and I am not copying the files into Galaxy. When I try to view the files in the library after uploading it takes a long time to load the library view (sometimes it times out), and when it does load it lists every file three times so instead of there being 180 fastq files in the library there are 540. I have tried this multiple times after deleting the library and starting over, and each time it looks like there are three copies of each file. Has anyone else had trouble uploading a large number of fastq files into a library at the same time? I tried to delete a bunch of the duplicate files but it just timed out. I ended up creating 6 libraries, and split the files between these with no problems. It seems there is a problem when uploading a large number of files into a single library. I could open the library maybe one time out of 6, the rest it would time out, and when it did open each file showed up three times. After I split between 6 different libraries they open almost instantly and each file shows up once. I am running the last dist release, not the most recent one. -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___ 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/ -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___ 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/ Greg Von Kuster Galaxy Development Team g...@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] Getting tool dirpath in a Python code file
On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida soft...@leandrohermida.com wrote: On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock p.j.a.c...@googlemail.com wrote: For standard Python tools in Galaxy, I'm using os.path.split(sys.argv[0])[0] to get the path, which on reflection probably should be written as os.path.dirname(sys.argv[0]) as you suggest. What do __file__ and sys.argv[0] give you? The simplest way to debug this is to add a print statement, since Galaxy will show the stdout. Hi Peter, __file__ throws an error: global name '__file__' is not defined I guess the script is being loaded as a string, and run with eval(...) or something like that. It would also explain why sys.argv[0] would be one of the Galaxy script files. os.path.abspath(os.path.dirname(sys.argv[0])) gives me /path/to/galaxy/scripts directory which is two levels up from what the tool directory I want for example /path/to/galaxy/tools/mytool So combine that with ../tools/mytool/ and you're done? OK, you have to know the name of the folder your tool *should* be in... so not a perfect solution. Peter ___ 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/
