galaxy-dev October 2011

galaxy-dev@lists.galaxyproject.org

90 participants
149 discussions

Problem cutting files
by Elizabeth Ashley 10 Nov '11

10 Nov '11

Dear Galaxy users I am trying to cut a tab delimited file using the cut option under text manipulation. When the columns I wish are cut out, the resultant file contains only '.' (dots) where the data was in the previous file. Any ideas how to resolve this problem? Lizzy

2 1

dropdown user-type
by Nikolai Vazov 09 Nov '11

09 Nov '11

Hi, I can't find out how to use the dropdown "User type" which is displayed after I select User > Register in the start page of Galaxy. Do I have to define the types myself? Are they pre-set? The dropdown menu just says "Select one", but the options are empty. Thank you in advance Nikolay -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

2 1

History reports misconfiguration of the Galaxy job running system
by Andrew Warren 09 Nov '11

09 Nov '11

Hello, I recently encountered a problem when trying to run Cufflinks on eight BAM files on our galaxy instance (via the multi-input toggle) and received the error: "Unable to run job due to a misconfiguration of the Galaxy job running system" for some, but not all, of the cufflinks jobs that appear in the history. These particular BAM files were copied over from the history of a larger workflow where they were successfully run through cufflinks. In the case of the problem workflow run, the cufflinks jobs are all successfully submitted to Torque PBS and continue to run and finish but many have this error displayed in the History. The jobs with the error displayed fail to copy files from the working directory to the database directory despite running to completion. We recently updated to galaxy-central changeset 6131:be6c89c33639. I have seen this error multiple times for this workflow, even after restarting galaxy. Does anyone have any ideas of what might be going wrong? Thanks for any help, Andrew Warren

2 3

Tool shed and datatypes
by Duddy, John 08 Nov '11

08 Nov '11

Can we introduce new file types via tools in the tool shed? It seems Galaxy can load them if they are in the datatypes configuration file. Does tool installation automate the editing of that file? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

3 14

manage_db.sh upgrade error
by Iry Witham 08 Nov '11

08 Nov '11

When I run sh manage_db.sh upgrade I get the following error: 2 -> 3... Traceback (most recent call last): File "./scripts/manage_db.py", line 55, in <module> main( repository=repo, url=db_url ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0003_security_and_libraries.py", line 423, in upgrade metadata.create_all() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 1796, in create_all bind.create(self, checkfirst=checkfirst, tables=tables) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1129, in create self._run_visitor(self.dialect.schemagenerator, entity, connection=connection, **kwargs) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1158, in _run_visitor visitorcallable(self.dialect, conn, **kwargs).traverse(element) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 89, in traverse return traverse(obj, self.__traverse_options__, self._visitor_dict) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 200, in traverse return traverse_using(iterate(obj, opts), obj, visitors) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 194, in traverse_using meth(target) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/compiler.py", line 829, in visit_metadata collection = [t for t in sql_util.sort_tables(tables) if self._can_create(t)] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/util.py", line 22, in sort_tables return topological.sort(tuples, tables) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/topological.py", line 32, in sort return [n.item for n in _sort(tuples, allitems, allow_cycles=False, ignore_self_cycles=True)] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/topological.py", line 209, in _sort raise CircularDependencyError("Circular dependency detected " + repr(edges) + repr(queue)) sqlalchemy.exc.CircularDependencyError: Circular dependency detected [(form_definition_current, form_definition), (library_item_info, library_folder_info_association), (library_item_info, library_item_info_element), (library_item_info, library_item_info_permissions), (library_item_info, library_dataset_dataset_info_association), (library_item_info, library_info_association), (library_item_info, library_dataset_info_association), (visualization_revision, visualization), (form_definition, external_service), (form_definition, form_values), (form_definition, request_type), (form_definition, run), (form_definition, form_definition_current), (history_dataset_association, job_to_input_dataset), (history_dataset_association, job_to_output_dataset), (history_dataset_association, implicitly_converted_dataset_association), (history_dataset_association, history_dataset_association_tag_association), (history_dataset_association, validation_error), (history_dataset_association, history_dataset_association_rating_association), (history_dataset_association, job_external_output_metadata), (history_dataset_association, history_dataset_association_annotation_association), (history_dataset_association, history_dataset_association_display_at_authorization), (history_dataset_association, metadata_file), (galaxy_user, stored_workflow_rating_association), (galaxy_user, stored_workflow_menu_entry), (galaxy_user, library_item_info), (galaxy_user, visualization_user_share_association), (galaxy_user, default_user_permissions), (galaxy_user, visualization_rating_association), (galaxy_user, dataset_tag_association), (galaxy_user, page_user_share_association), (galaxy_user, library_dataset_info_association), (galaxy_user, user_action), (galaxy_user, history), (galaxy_user, library_info_association), (galaxy_user, history_dataset_association_tag_association), (galaxy_user, workflow_step_tag_association), (galaxy_user, history_dataset_association_rating_association), (galaxy_user, page), (galaxy_user, history_rating_association), (galaxy_user, stored_workflow), (galaxy_user, history_annotation_association), (galaxy_user, user_role_association), (galaxy_user, api_keys), (galaxy_user, request), (galaxy_user, history_user_share_association), (galaxy_user, user_address), (galaxy_user, library_dataset_dataset_association), (galaxy_user, history_tag_association), (galaxy_user, page_rating_association), (galaxy_user, library_dataset_dataset_info_association), (galaxy_user, library_folder_info_association), (galaxy_user, visualization_tag_association), (galaxy_user, stored_workflow_user_share_connection), (galaxy_user, galaxy_session), (galaxy_user, visualization), (galaxy_user, history_dataset_association_display_at_authorization), (galaxy_user, job), (galaxy_user, galaxy_user_openid), (galaxy_user, event), (galaxy_user, stored_workflow_tag_association), (galaxy_user, stored_workflow_annotation_association), (galaxy_user, user_preference), (galaxy_user, workflow_step_annotation_association), (galaxy_user, page_annotation_association), (galaxy_user, history_dataset_association_annotation_association), (galaxy_user, page_tag_association), (galaxy_user, user_group_association), (galaxy_user, visualization_annotation_association), (sample, sample_dataset), (sample, sample_run_association), (sample, sample_event), (workflow_invocation, workflow_invocation_step), (history, job), (history, history_annotation_association), (history, job_export_history_archive), (history, history_tag_association), (history, history_dataset_association), (history, job_import_history_archive), (history, default_history_permissions), (history, history_user_share_association), (history, history_rating_association), (history, event), (history, galaxy_session_to_history), (history, galaxy_session), (history, sample), (run, sample_run_association), (run, request_type_run_association), (request_type, sample_state), (request_type, request_type_permissions), (request_type, request_type_run_association), (request_type, request_type_external_service_association), (request_type, request), (page, page_tag_association), (page, page_user_share_association), (page, page_revision), (page, page_rating_association), (page, page_annotation_association), (stored_workflow, workflow), (stored_workflow, stored_workflow_rating_association), (stored_workflow, stored_workflow_menu_entry), (stored_workflow, stored_workflow_tag_association), (stored_workflow, stored_workflow_annotation_association), (stored_workflow, stored_workflow_user_share_connection), (library_dataset_dataset_association, library_dataset_dataset_info_association), (library_dataset_dataset_association, job_to_output_library_dataset), (library_dataset_dataset_association, job_external_output_metadata), (library_dataset_dataset_association, library_dataset_dataset_info_template_association), (library_dataset_dataset_association, library_dataset_dataset_association_permissions), (library_dataset_dataset_association, implicitly_converted_dataset_association), (request, sample), (request, request_event), (post_job_action, post_job_action_association), (workflow, workflow_step), (workflow, workflow_invocation), (galaxy_session, job), (galaxy_session, galaxy_user_openid), (galaxy_session, user_action), (galaxy_session, galaxy_session_to_history), (galaxy_session, event), (visualization, visualization_user_share_association), (visualization, visualization_tag_association), (visualization, visualization_rating_association), (visualization, visualization_revision), (visualization, visualization_annotation_association), (workflow_step, workflow_invocation_step), (workflow_step, workflow_step_connection), (workflow_step, workflow_step_annotation_association), (workflow_step, workflow_step_tag_association), (workflow_step, workflow_output), (workflow_step, post_job_action), (sample_state, sample_event), (job, post_job_action_association), (job, job_to_output_library_dataset), (job, job_to_output_dataset), (job, job_export_history_archive), (job, job_to_input_dataset), (job, job_import_history_archive), (job, job_parameter), (job, job_external_output_metadata), (job, workflow_invocation_step), (job, task), (form_values, external_service), (form_values, run), (form_values, galaxy_user), (form_values, request), (form_values, sample), (external_service, sample_dataset), (external_service, request_type_external_service_association), (page_revision, page)][]

2 2

Re: [galaxy-dev] Inquiring
by Nate Coraor 07 Nov '11

07 Nov '11

Hi Yan, I've again moved this back to the galaxy-dev list. Please reply to this list and not galaxy-user. Yan Luo wrote: > Dear Nate, > > Thanks for your quick response. I appreciate, it is very important for us to > use it. We have problem recently. > > (1) In fact, I can't find the file "paster.log". The problem is that > recently we expanded our gluster(Linux sever) and did the rebalance that has > some bugs. Some of files permission have been changed. So we can't use > User/register righr now, when we tried, we got the sever error, do you have > any idea how to fix it? (we can change the ownships/read and write > permission for some files manually, but we don't know which files and where > they are?) If you are executing run.sh without the --daemon flag, the output will go to whatever terminal window you started Galaxy in, not to a file. You'll want to make sure that all of the files under Galaxy's root directory are owned by a single user, which is the same user which starts and runs the Galaxy process. > (2) We want to reboot the Galaxy, should we first stop and start as > follows? > $ sh run.sh --stop > $ sh run.sh The full command to stop would be `sh run.sh --stop-daemon`, but that only applies if you originally started Galaxy with `run.sh --daemon`. > Is there any difference if I use "-daemon" flag? Last times, my colleague > started using "./run.sh". How to stop it? > If "$ sh run.sh --stop" doesn't work (I didn't try yet, ), how can I find > the process (Linux) that is running by Galaxy and kill it? The --daemon flag runs Galaxy in the background and redirects its output to paster.log. Without the --daemon flag, the process stays connected to the terminal in which you start it. Since Galaxy wasn't originally started with the --daemon flag, you'll need to find the process, either by locating the terminal window in which it was started (possibly by your colleague) and then hitting Ctrl-C, or by using the `ps` command (e.g. `ps auxwww | grep python`) and killing the Galaxy process. It usually looks something like: nate 18213 0.9 0.4 438844 146260 pts/7 Sl+ 10:47 2:30 python ./scripts/paster.py serve universe_wsgi.ini So you would do: % kill 18213 > (3) Could you please let me know if there is a default administrator > user/password for galaxy. I want to add an administrator user, how can I do > that? > According to the instruction, I will change a line of "universe_wsgi.ini" as > follows. How can I set/get my password? > admin_users = yan.luo(a)email.com There is no default. Any users set in admin_uesrs will be administrators. If the account specified in admin_users does not yet exist, you can simply create it. Once created, that account will be an administrator. > (4) I found our "universe_wsgi.ini" contains the following setting, should I > remove "#" before this line, stop and start galaxy? > #allow_user_creation = True No, True is the default setting so with it commented it is still set to True. > I plan to restart our galaxy, if it is possible, could you please let me > know your phone #? I can call you sometime today, or if you prefer, I can > give you my phone #. Unfortunately, we don't have the resources for phone support. We'll be happy to help via email as much as possible. --nate > > Looking forward to hearing from you. > > Best Wishes, > > Yan Luo, Ph.D. > NIH > > > On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > > > Hi Yan, > > > > I've moved this discussion to the galaxy-dev list since it pertains to a > > local installation of Galaxy. > > > > Responses to your questions follow, in-line. > > > > Yan Luo wrote: > > > Dear Sir, > > > > > > (1)We installed Galaxy, but recently the user can't registered and got > > the > > > following error, how can we fix it? > > > > > > Sever error > > > An error occurred. See the error logs for more information.(To turn debug > > on > > > to display ...). > > > > Since debug = False in universe_wsgi.ini, you should be able to find a > > more detailed error message in the log file. If starting Galaxy with: > > > > % sh run.sh --daemon > > > > The default log file is 'paster.log' in Galaxy's root directory. > > > > > (2) Could you please let me know if there is any command to stop galaxy? > > > > If starting with the --daemon flag (as above), you can use: > > > > % sh run.sh --stop-daemon > > > > If running in the foreground, you can use Ctrl-C to terminate the > > process. There is a recent bug whereby Ctrl-C is ineffective on some > > platforms under Python 2.6 - in this case you will have to kill/pkill > > the process manually. We are working on a fix for the latter. > > > > > (3) If I reset universe_wsgi.ini file and want to set an administrator > > > user(I can add a line in the above file), how can I get the password? > > Should > > > I stop galaxy(See question 2) first? then run "./setup.sh" and > > "./run.sh". > > > > setup.sh would have only been necessary prior to running Galaxy the > > first time, however, this step has recently been removed. If you are > > referencing documentation that still refers to setup.sh, please let us > > know so we can update it - I did notice this was still on the > > "Production Server" page, so I removed it from there. > > > > You no longer need to run setup.sh at all. > > > > > (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be > > generated? > > > if I want to change this file,should I edit it before "run.sh" and after > > > "setup.sh". Is it right? > > > > setup.sh and its replacements in run.sh and the Galaxy application > > itself never overwrite files, they only create files from sample files > > if they do not exist. > > > > > (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and > > > "./setup.sh"(./run.sh), which one is correct under Linux? > > > > Both syntaxes are effectively the same in most cases. > > > > --nate > > > > > > > > Looking forward to hearing from you. > > > > > > Best Wises, > > > > > > Yan Luo, Ph.D. > > > NIH > > > < > > http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way, > > > > > > > > _______________________________________________ > > > galaxy-user mailing list > > > galaxy-user(a)lists.bx.psu.edu > > > http://lists.bx.psu.edu/listinfo/galaxy-user > > > >

3 38

Server Error after Update
by SHAUN WEBB 07 Nov '11

07 Nov '11

Hi, I updated my test server today and everything seemed fine. I added a new library item via a URL. After that my history panel displays "Internal Server Error" and I am getting the error below in paster.log: Any ideas how this has occurred and if there is a fix? Shaun ---------------------------------------- Exception happened during processing of request from ('2.218.9.31', 63227) Traceback (most recent call last): File "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__ self.handle() File "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 125, in wsgi_write_chunk "Content returned before start_response called") RuntimeError: Content returned before start_response called -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

ImportError: No module named galaxy
by Oren Livne 07 Nov '11

07 Nov '11

Dear All, I am running the example_watcher_folder.py API script and it intermittently fails to run a workflow on a file dropped into the import directory (the file is imported and the workflow starts running, but its jobs hang or fail). Galaxy uses a condor dramaa job runner. When I look at the galaxy script being run by condor, it sets the PYTHONPATH and then executes the following command, which also fails at the command line. galaxy@vm-debian:~/galaxy-dist$ python /home/galaxy/galaxy-dist/tools/filters/sorter.py --input=/tmp/galaxy/datafiles/000/dataset_105.dat --out_file1=/tmp/galaxy/datafiles/000/dataset_106.dat --column=7 --style=num --order=DESC Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/filters/sorter.py", line 15, in <module> from galaxy import eggs ImportError: No module named galaxy How can I resolve this error? I would like to be able to test such commands at the command line, as well as ensure that galaxy workflows run reliably. Thanks, Oren

2 3

last hurdle
by Robert Day 07 Nov '11

07 Nov '11

Hi, Sorry to bother you guys with such a simple thing. I'm quite new to the terminal and command line etc. so downloading and getting Galaxy running on my PC was a voyage of discovery! Anyhow, I have it, it's alive.......... just can't get any data in! Have made myself an Admin User to create a data library, I point the importer at the files and it starts but never stops and remains at 0bytes. Have I forgotten to set something up? Surely I can just dump all my files in a folder in the right place and go get it when I need it. Can't seem to find an idiots guide for setting this up for a local install (just me and my computer). Any pointers or helpful threads would be great. Cheers Rob Sent from my PC

3 2

Clusters, Runners, and user credentials
by Lloyd Brown 04 Nov '11

04 Nov '11

I'm a systems administrator for an HPC cluster, and have been asked by a faculty member here to try to get galaxy to work on our cluster. Unfortunately, there are one or two outstanding questions that I can't seem to find the answer to, and I'm hoping someone here can help me out. In particular, is galaxy, and the PBS runner specifically, capable of submitting jobs under specific user names? Essentially, if I set up galaxy to push jobs to our cluster, will they all show up under one user credential (eg. the "galaxy" user), or can we set it up so that the user logged into galaxy, is used to submit the job? This one is kindof a show-stopper, since our internal policies require that all jobs have a specific user credential, with one person per username. Thanks, Lloyd -- Lloyd Brown Systems Administrator Fulton Supercomputing Lab Brigham Young University http://marylou.byu.edu

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galaxy-dev October 2011