galaxy-dev November 2011

galaxy-dev@lists.galaxyproject.org

83 participants
157 discussions

IWSG-Life 2012 (4th International Workshop on Science Gateways for Life Sciences)
by Dave Clements 08 Nov '11

08 Nov '11

Hello all, A conference announcement that may be of interest if you are hosting your own Galaxy instance. A couple of Galaxy instances were discussed at the 2011 meeting (see https://sites.google.com/a/staff.westminster.ac.uk/iwsg-life2011/system/app… ). Dave C -------------------------------------------------------------------------------- IWSG-Life 2012 (4th International Workshop on Science Gateways for Life Sciences) Workshop Website: http://iwsg-life.org/2012 Date: 23-25 May 2012 Place: Amsterdam, The Netherlands Important dates: The deadline for paper/abstract submission: 16 January 2012 Notification of acceptance: 14 February 2012 Submission of camera ready papers: 19 March 2012 The workshop will take place in conjunction with the Healthgrid Conference 2012 (http://amsterdam2012.**healthgrid.org/<http://amsterdam2012.healthgrid.org/> ) and featuring EGI.eu. Scope: IWSG-Life'12 will bring together scientists from the field of life sciences, bioinformatics and computer science. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of Science Gateways. We invite the submission of papers related to various aspects of molecular and systems biology and Science Gateways/Portals. Suggested topics include, but are not limited to: * Management of biological high-throughput data * Modeling protein-carbohydrate recognition * Machine learning for computational immunomics * Molecular simulations for drug discovery * Portal technology and portal construction methods * Usage models and gateway tools for life sciences * Security aspects of Science Gateways for life sciences * Usability studies of life sciences portals/gateways * Workflows and service composition for life sciences * Service discovery and ontologies for life sciences * Tools for managing grid and cloud portability * Integration of life sciences with e-infrastructures * Demonstrations/ success stories Call for papers There are three alternatives for researchers to present their work: talks, lightning talks, and demonstration sessions. Submission of a full paper may result in a talk, submission of an abstract may result in an lightning talk or a demonstration. Accepted full papers will be published in PubMed-listed proceedings together with the proceedings of the Healthgrid Conference 2012. Full papers All full papers will be double-blind peer reviewed and evaluated on quality and relevance. All submissions are held in confidentiality prior to publication in the proceedings. Presenters will be given a 20-minute time slot (plus 5 minutes for questions) to provide a summary and update to their work. Papers will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site at https://www.easychair.org/**conferences/?conf=hgiwsg2012<https://www.easychair.org/conferences/?conf=hgiwsg2012>. They have to be formatted according to the layout style required by the IOSPress. Formatting requirements can be found at: http://www.iospress.nl/authco/**instruction_crc.html<http://www.iospress.nl/authco/instruction_crc.html>. The paper length must not exceed ten pages and the papers must be written in clear and readable English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. Abstracts Abstracts can be submitted for the lightning talk or for the demonstration sessions. Authors must indicate clearly which presentation format they are aiming for. All abstracts will be double-blind peer reviewed and evaluated on quality and relevance. Accepted lightning talk submissions will be given a 10-minute time slot (plus 5 minutes for questions) in an lightning talk session. Accepted demonstration submissions will be given a 10-minute time slot (plus 5 minutes for questions) in a demonstration session. Demonstrations will be given live to the workshop audience. Abstracts will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site at https://www.easychair.org/**conferences/?conf=hgiwsg2012<https://www.easychair.org/conferences/?conf=hgiwsg2012>. The abstract length must not exceed 200 words and the abstracts must be written in clear and readably English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Re: [galaxy-dev] [OPEN] Pull request #1 for galaxy/galaxy-dist: locale files in Chinese
by Greg Von Kuster 08 Nov '11

08 Nov '11

Hello, Thanks very much for contributing locale files for Chinese. I've added your contribution to the distribution in change set revision 6248:bc399a95e31e, which should be available in the distribution within the next few weeks. I downloaded the raw files and committed them instead of accepting your pull request because your repository is a fork of galaxy-dist and in order to accept the pull request is must be a fork of galaxy-central. Thanks very much for your contribution! On Nov 4, 2011, at 8:25 AM, Bitbucket wrote: > A new pull request has been opened by hanfeisun. > > hanfeisun/galaxy-dist-i18n-chinese has changes to be pulled into galaxy/galaxy-dist. > > https://bitbucket.org/galaxy/galaxy-dist/pull-request/1/locale-files-in-chi… > > Title: locale files in Chinese > > I wrote 4 locale files such as ginga.po/mo and tools.po/mo ,tried them on my server and it worked well. > > > > > Changes to be pulled: > > 3b384a62d359 by hanfeisun: "Add locale files for Chinese" > > > -- > This is an issue notification from bitbucket.org. > You are receiving this either because you are the participating > in a pull request, or you are following it. > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Looks like actual user breaks splitting
by Chorny, Ilya 08 Nov '11

08 Nov '11

Hey John, Any thoughts? Ilya Traceback (most recent call last): File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/runners/tasks.py", line 73, in run_job tasks = splitter.do_split(job_wrapper) File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/splitters/multi.py", line 73, in do_split input_type.split(input_datasets, get_new_working_directory_name, parallel_settings) File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/datatypes/data.py", line 473, in split raise Exception("Text file splitting does not support multiple files") Exception: Text file splitting does not support multiple files Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Re: [galaxy-dev] Installing Galaxy on local server
by Jennifer Jackson 08 Nov '11

08 Nov '11

Hello Tuqa, Galaxy will not stop by itself. That said, you will want to monitor the instance and any associated cluster, just as you would any other important processes. Please send all follow-up with a cc to the mailing list ("reply-all"). The development community is a great resource for administrative advice and they may have more to add to this reply, i.e. how stable they have found Galaxy to be under various conditions. Best, Jen Galaxy team On 11/8/11 4:01 AM, Toqa Manasrah wrote: > Thank you so much, > > I did the installation and I ran it under my server. > I have one thing concerning about now. if u can help plz. > > how to run Galaxy in such way that the html interface will continuously working and available for all users visiting the page? > > i mean how to guarantee that the "sh run.sh" will keep running without any interrupt? > > Thank you, > Tuqa > > ________________________________________ > From: Jennifer Jackson [jen(a)bx.psu.edu] > Sent: Thursday, November 03, 2011 6:47 PM > To: Toqa Manasrah > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Installing Galaxy on local server > > Hello Toqa, > > From your description, this sounds like a local installation for the > Galaxy instance itself. Then you can add on a cluster (local or cloud) > as needed. > > Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/ > Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed > > Hopefully the documentation is helpful, > > Best, > > Jen > Galaxy team > > On 11/3/11 9:40 AM, Toqa Manasrah wrote: >> Hello, >> >> I am a graduate student at GSU. I am looking for installing GALAXY on >> our local server http://alla.cs.gsu.edu/~software. as a result I like my >> server homepage start with the GALAXY interface, like this one: >> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some >> software tolls that we developed in ourdepartment. my primary question >> is which option Ihave to choose: Local or cloud? >> >> looking forward for your help and directions. >> >> Thank you. >> >> Tuqa >> >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Re: [galaxy-dev] [galaxy-user] number of concurrent jobs/user
by Nate Coraor 08 Nov '11

08 Nov '11

On Nov 8, 2011, at 3:01 AM, Petr Novak wrote: > Is it possible to limit number of concurrent jobs when job_runner is pbs? The setting in universe_wsgi.ini is obviously limiting only locally run jobs. Hi Petr, I've moved this over to the galaxy-dev list since it concerns a local installation. There's an undocumented option named user_job_limit which will limit the number of jobs run by a single user. You can limit the total number of jobs running by the entire Galaxy system by using the resource controls in PBS itself. --nate > > Petr > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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Re: [galaxy-dev] last hurdle
by Nate Coraor 08 Nov '11

08 Nov '11

On Nov 7, 2011, at 10:41 PM, Robert Day wrote: > No but worked round it by enabling the directory path load option in the .ini. This worked fine. > > On a different note....if I want to install the missing tools eg bowtie should they just work if they are already on my computer and in my path? Do I have to point galaxy to them or their index files etc? > > I have been using bowtie, samtools, fastqc etc from terminal. Hi Rob, That they're on your $PATH is enough to execute them. Most can work with a reference genome in your history, but for larger ones (or those that you'd be using frequently) it's best to pre-build indexes and set up the paths to those indexes: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup --nate > > Rob > > Sent from my iPad > > On 8/11/2011, at 9:51 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > >> On Oct 21, 2011, at 7:55 PM, Robert Day wrote: >> >>> 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. >> >> Hi Rob, >> >> Sorry for the delay in response. Were you ever able to successfully upload files to your local instance? >> >> --nate >> >>> >>> Cheers Rob >>> Sent from my PC >>> ___________________________________________________________ >>> 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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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

an attempt on multiple multiple inputs
by Andrew Warren 07 Nov '11

07 Nov '11

Hello galaxy dev, I have done some work on enabling multiple input files for multiple tool parameters in a workflow. This could come in handy when running multiple paired end data files for RNA Seq through a pipeline (I know this has been discussed on a few different threads but I couldn't find any when writing this up). The changes cause the workflow controller to step through the input data in synchronized fashion going down the list (of selected inputs). When running a workflow with multiple, multiple inputs the default ordering from the history can be problematic so I also did a little work on a new display/interaction method that I called "on_deck." If you set the tool xml config to have parameter tag display="on_deck" then it will enable this interaction method. e.g. from the bowtie wrapper: <when value="paired"> <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores" display="on_deck"/> <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file" display="on_deck"> The changes to run.mako seem a little hacked in to me (I am still getting a handle on the mako format). I wasn't sure where to stick the javascript that is in there. It only lets you go forward if the number of inputs, for all multiple toggled inputs, is equal. The code is at https://bitbucket.org/aswarren/galaxy-cid 8cf8d25557b2 Hope this helps somebody. Andrew Warren

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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.

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galaxy-dev November 2011