November 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] tool_id for tool_shed tools
by Greg Von Kuster 16 Nov '12

16 Nov '12

Similar entries for other tool shed tools that are installed into a Galaxy instance using the Galaxy Admin interface (not the tool migration stage process) are available in the shed_tool_con.xml file (or whatever shed-related files you have defined in your Galaxy config). You can also find tool ids for all of the tools loaded into your Galaxy tool panel by inspecting the single file name integrated_tool_conf.xml. Using this file, you won't have to inspect more than the single file. These files are all described in the tool shed wiki at the following page. http://wiki.galaxyproject.org/GalaxyToolPanel Greg Von Kuster On Nov 16, 2012, at 2:52 AM, Andreas Kuntzagk wrote: > Thanks, that helps in this case. > But I might also need the ids for other toolshed tools to adjust the job runner settings. > > Andreas > > On 15.11.2012 15:23, Greg Von Kuster wrote: >> Hi Andreas, >> >> Assuming you have executed the migration process for the tools so they are now installed into your Galaxy instance from the tool shed, you can check the entries in the migrated_tools_conf.xml file and get the ids. Entries will look something like the following where you can get the id from the <id> tag. >> >> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/e0232cbac965/picard/rgPicardMar…" guid="toolshed.g2. >> bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0"> >> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> >> <repository_name>picard</repository_name> >> <repository_owner>devteam</repository_owner> >> <installed_changeset_revision>e0232cbac965</installed_changeset_revision> >> <id>toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0</id> >> <version>1.56.0</version> >> </tool> >> >> Greg Von Kuster >> >> >> On Nov 15, 2012, at 9:10 AM, Andreas Kuntzagk wrote: >> >>> Hi, >>> >>> I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over the tool name and write down the id? >>> >>> regards, Andreas >>> >>> -- >>> Andreas Kuntzagk >>> >>> SystemAdministrator >>> >>> Berlin Institute for Medical Systems Biology at the >>> Max-Delbrueck-Center for Molecular Medicine >>> Robert-Roessle-Str. 10, 13125 Berlin, Germany >>> >>> http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich >>> ___________________________________________________________ >>> 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/ >> > > -- > Andreas Kuntzagk > > SystemAdministrator > > Berlin Institute for Medical Systems Biology at the > Max-Delbrueck-Center for Molecular Medicine > Robert-Roessle-Str. 10, 13125 Berlin, Germany > > http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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cannot start galaxy after upgade
by Anne Pajon 15 Nov '12

15 Nov '12

Hi, I'm having some problems restarting our galaxy server after upgrading it to the latest version today... Here is the error message: python path is: /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Babel-0.9.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg, /opt/local/home/webapp/galaxy/lib, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload, /opt/local/home/webapp/software/mercurial/mercurial-2.1/lib/python2.7/site-packages, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,841 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-11-15 14:12:54,884 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-11-15 14:12:54,975 At database version 107 galaxy.tool_shed.migrate.check DEBUG 2012-11-15 14:12:54,991 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/local/home/webapp/galaxy/lib/galaxy/app.py", line 47, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/check.py", line 56, in verify_tools tool_shed_accessible, missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/common.py", line 46, in check_for_missing_tools tool_dependencies_dict = tool_shed_decode( text ) File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/encoding_util.py", line 15, in tool_shed_decode a, b = value.split( ":" ) ValueError: too many values to unpack Removing PID file paster.pid Any help would be greatly appreciated. Thanks! Cheers, Anne. -- Anne Pajon, Ph.D. - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon(a)cruk.cam.ac.uk | +44 (0)1223 40 4334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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Fix for KeyError in templates/show_params.mako
by Jim Johnson 15 Nov '12

15 Nov '12

A user encountered a KeyError when clicking the "View Details" icon from an older Cuffdiff history item: File '/galaxy/PRODUCTION/database/compiled_templates/show_params.mako.py', line 106 in render_body __M_writer(unicode( inputs_recursive(tool.inputs, params_objects, depth=1) )) File '/galaxy/PRODUCTION/database/compiled_templates/show_params.mako.py', line 33 in inputs_recursive return render_inputs_recursive(context.locals_(__M_locals),input_params,param_values,depth) File '/galaxy/PRODUCTION/database/compiled_templates/show_params.mako.py', line 202 in render_inputs_recursive __M_writer(unicode(input.value_to_display_text(param_values[input.name], trans.app))) KeyError: 'multiread_correct' This can be fixed in templates/show_params.mako by checking if the input.name key exists in the param_values, surrounding the contents of the for loop with: %if input.name in param_values: %endif $ hg diff templates/show_params.mako diff -r 340438c62171 templates/show_params.mako --- a/templates/show_params.mako Wed Nov 14 18:50:20 2012 -0500 +++ b/templates/show_params.mako Thu Nov 15 08:15:47 2012 -0600 @@ -12,23 +12,25 @@ <%def name="inputs_recursive( input_params, param_values, depth=1 )"> %for input_index, input in enumerate( input_params.itervalues() ): - %if input.type == "repeat": - %for i in range( len(param_values[input.name]) ): - ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } - %endfor - %elif input.type == "conditional": - <% current_case = param_values[input.name]['__current_case__'] %> + %if input.name in param_values: + %if input.type == "repeat": + %for i in range( len(param_values[input.name]) ): + ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } + %endfor + %elif input.type == "conditional": + <% current_case = param_values[input.name]['__current_case__'] %> + <tr> + ${ inputs_recursive_indent( text=input.test_param.label,depth=depth )} +  + <td>${input.cases[current_case].value}</td> + </tr> + ${ inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth+1) } + %elif getattr(input, "label", None): <tr> - ${ inputs_recursive_indent( text=input.test_param.label,depth=depth )} -  - <td>${input.cases[current_case].value}</td> + ${inputs_recursive_indent( text=input.label,depth=depth )} + <td>${input.value_to_display_text(param_values[input.name], trans.app)}</td> </tr> - ${ inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth+1) } - %elif getattr(input, "label", None): - <tr> - ${inputs_recursive_indent( text=input.label,depth=depth )} - <td>${input.value_to_display_text(param_values[input.name], trans.app)}</td> - </tr> + %endif %endif %endfor </%def>

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Working with files outside galaxy without copying?
by Samuel Lampa 15 Nov '12

15 Nov '12

Hi, We are looking into ways to integrate galaxy into the workflows of users at our cluster, with lots of NGS users running all and any kind of analyses on their typically huge amounts of data. For this we use a parallel file system, available on all compute nodes. This file system, although approx 1PB in size, is constantly filling up, and thus we are not very attracted by the idea of copying files into/out of galaxy for each analysis. Thus, we would be interested to know what are the options for working with existing/external(to galaxy) file systems? Eg. would it be possible to link files into some kind of galaxy file system (I'm not totally clear about how galaxy stores it's data, although I found out that stuff is created in database/files), from outside? ... or is there any work going on for selecting any file system path as input in galaxy workflows? ... or any other hints? As said, I'm quite new to galaxy, trying to grok my head around how we can use it, so all hints are welcome. Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se Twitter - twitter.com/samuellampa Blog - saml.rilspace.org G+ - gplus.to/saml

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Re: [galaxy-dev] Is there any timeout in Galaxy
by Dave Clements 15 Nov '12

15 Nov '12

Hi Akshay, I don't know the answer to your question. So: 1) I went to http://galaxyproject.org/search/web/ and searched for "timeout" and then "timeout workflow." There are lots of email threads (and I learned some stuff :-), but I didn't find a direct answer to your question. 2) I'm sending your question to the galaxy-dev list where it will be seen by hundreds of galaxy admins and tool developers. (And this thread will also be found by any future searches.) Thanks, Dave C On Thu, Nov 15, 2012 at 8:33 AM, <akshaychoche(a)gmail.com> wrote: > Hello, > > My name is Akshay and I am a computer science graduate student at UGA in > Dr. Kissinger's Lab. We have created an extension to galaxy which allowed > users to add web services as tools into galaxy, these could be either used > as stand-alone or in a workflow. I wanted to know if Galaxy employs any > time out strategy. > > Consider a case where I have a workflow with BLASTP now it takes some time > to run blast and then get result form it. When I try that experiment as > standalone (i.e., running the run method first and then after several mins > getting result using job id works) however when I create a workflow in > which one tool being run method of blast followed by getresult, galaxy > seems to time out. > > Would appreciate your feedback on the same. > > -Akshay Choche > Graduate Research Assistant (Kissinger Research Group) > Center for Tropical and Emerging Global Diseases > The University of Georgia, > Athens, GA - 30605 > Tele: 256-520-6541 > Email: achoche(a)uga.edu, akshaychoche(a)gmail.com > http://www.cs.uga.edu/~choche > -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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tool_id for tool_shed tools
by Andreas Kuntzagk 15 Nov '12

15 Nov '12

Hi, I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over the tool name and write down the id? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Database upgrade 108 and SQLite
by Peter Cock 15 Nov '12

15 Nov '12

Hi all, Is this likely to cause problems using Galaxy on SQLite (the default and very handy for a development machine)?: $ sh manage_db.sh upgrade 107 -> 108... Add the ExtendedMetadata and ExtendedMetadataIndex tables SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html No handlers could be found for logger "0108_add_extended_metadata" done Thanks, Peter

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Display of HTML type broken in new Galaxy ?
by Lukasse, Pieter 15 Nov '12

15 Nov '12

Hi, I noticed that in the new Galaxy version the preview of HTML files seems to be broken. When I try to preview a HTML file generated by a tool, it displays a HTML that has all style "stripped off". So the HTML display is in fact changing the generated HTML before displaying it. Has anyone noticed this as well? What are the fixes/workarounds? [cid:image001.jpg@01CDAC4F.72D92640] Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Join (Operate on Genomic Intervals)
by George Maliha 14 Nov '12

14 Nov '12

Hello, I am using the Galaxy public server to conduct a join operating on genomic intervals. However, my job has not completed in over 2 days. Is there a bug, and what can I do to speed up the process? Thank you, George

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ftp file upload error question
by Tony Szempruch 14 Nov '12

14 Nov '12

Dear Galaxy Devs, I have tried to upload 2 files though the ftp upload using FileZila. I have been getting the following error: Response: 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [::ffff:128.118.250.4] Command: USER ************** Response: 331 Password required for ************** Command: PASS ***** Response: 530 Sorry, the maximum number of clients (3) for this user are already connected. Error: Critical error Error: Could not connect to server I have seen that some one else had this issue and posted online. What should I do to try to get around this issue? Thank you Tony Szempruch

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