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Ignoring white space differences in test output
by Peter Cock 05 Apr '11

05 Apr '11

Hi all, I'd like to write a tool test where the sample output and the generated output are the same except for white space. i.e. running diff with the -w switch reports no differences. Is this possible at the moment with the Galaxy test framework? I'm hoping for a <test> <output> attribute. I don't see anything like this mentioned here: https://bitbucket.org/galaxy/galaxy-central/wiki/WritingTests Thanks, Peter

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Alternative Bowtie/TopHat tools
by Assaf Gordon 04 Apr '11

04 Apr '11

Still very much work-in-progress, but I'd like to hear any comments or ideas that you might have. No need to install, just visit here to see TopHat's interface: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_se1 Main differences from the existing TopHat tool: 1. Far fewer visible options 2. Select "Existing gene mode" (use GTF file) or do De-novo junction detection (or both) 3. Allow insertions/deletions detection (with the latest tophat). 4. Allow user to specify custom command line parameters. 5. Accepts Fasta, FastqSanger, FastqIllumina (but not generic "fastq", per your feedback). If you think there are other critical and often used options, let me know. updated code is available here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_1.tar.bz2 -gordon

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Password input field for tools?
by Daniel Schmidt 04 Apr '11

04 Apr '11

Hi all! Is there any way to use password input fields ("<input type="password"...") with tools? A tools XML definition file only seems to support text and textarea fields. I already tried setting a tools parameter type to "password", which unfortunately results in an "Unknown tool parameter type 'password'". Trying "password="True"" (like "area="True"") does not result in an error, but the text field is still just a normal text field. I may be mistaken, as I am new to Python and Galaxy, but there already seems to be a PasswordField class and a TextField class, which both can be found in several files. Was the PasswordField class for tool parameters maybe disabled for a reason? Thanks! Daniel

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Server error from history view
by Sarah Diehl 04 Apr '11

04 Apr '11

Hi all, I encounter the same error that was already mentioned in this list (with the same email title). For me it also does only happen when debug is set to false. However I could not find a solution to it in the archive of the mailing list. I tried it with both galaxy-dist and galaxy-central, newest version. The error is as follows: 10.1.5.190 - - [10/Mar/2011:11:41:20 +0200] "GET /history HTTP/1.1" 500 - "http://solweb2/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.14) Gecko/20110301 Fedora/3.6.14-1.fc14 Firefox/3.6.14" Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable URL: http://solweb2/history File '/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 154 in __call__ return body( environ, start_response ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 676 in render template.render_context( context ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 146 in render_context runtime._render_context(self, self.callable_, context, *args, **kwargs) 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/root/history.mako.py', line 55 in render_body __M_writer(u'\n<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\n\n<html>\n\n<head>\n<title>') File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 673 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=f611411aa8a0c665eb9e71b6b35ec98d69a19a7826eff47d201855aea491539e3c45f483349e57b4' HTTP_HOST: 'solweb2' HTTP_REFERER: 'http://solweb2/' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.14) Gecko/20110301 Fedora/3.6.14-1.fc14 Firefox/3.6.14' HTTP_X_FORWARDED_FOR: '10.1.5.190' HTTP_X_FORWARDED_HOST: 'solweb2' HTTP_X_FORWARDED_SERVER: 'solweb2' ORGINAL_HTTP_HOST: 'localhost:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history' REMOTE_ADDR: '10.1.5.190' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- __file__: '/galaxy/galaxy_server/universe_wsgi.ini' admin_users: 'diehl@immunbio.mpg.de,lims_mq@solweb1.immunbio.mpg.de' allow_library_path_paste: 'True' allow_user_creation: 'True' allow_user_deletion: 'False' cookie_path: '/' database_connection: 'postgres://galaxy:galaxy@localhost/galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' datatypes_config_file: 'datatypes_conf.xml' debug: 'False' enable_api: 'True' enable_sequencer_communication: 'True' file_path: 'database/files' gbrowse_display_sites: 'wormbase,tair,modencode_worm,modencode_fly' genetrack_display_sites: 'main,test' here: '/galaxy/galaxy_server' id_secret: 'MPI IMMUNBIOLOGIE' library_import_dir: '/galaxy/galaxy_server/data' log_actions: 'True' log_events: 'True' log_level: 'DEBUG' new_file_path: 'database/tmp' new_user_dataset_access_role_default_private: 'True' require_login: 'False' static_cache_time: '360' static_dir: '/galaxy/galaxy_server/static/' static_enabled: 'True' static_favicon_dir: '/galaxy/galaxy_server/static/favicon.ico' static_images_dir: '/galaxy/galaxy_server/static/images' static_scripts_dir: '/galaxy/galaxy_server/static/scripts/' static_style_dir: '/galaxy/galaxy_server/static/june_2007_style/blue' tool_config_file: 'tool_conf.xml' tool_data_path: 'tool-data' tool_path: 'tools' ucsc_display_sites: 'main,test,archaea,ucla' use_interactive: 'False' use_lint: 'False' use_profile: 'False' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x63ab690> paste.cookies: (<SimpleCookie: galaxysession='f611411aa8a0c665eb9e71b6b35ec98d69a19a7826eff47d201855aea491539e3c45f483349e57b4'>, 'galaxysession=f611411aa8a0c665eb9e71b6b35ec98d69a19a7826eff47d201855aea491539e3c45f483349e57b4') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x692eb50> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x263ad90> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ Any help would be greatly appreciated. Best regards, Sarah

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Anyone configured authentication on nginx?
by Joe Cruz 04 Apr '11

04 Apr '11

Hello, Has anyone configured external authentication on nginx and if so could you please share your configuration? Thanks, Joe

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Anyone has tools for NCBI Lite-SRA format ?
by Assaf Gordon 04 Apr '11

04 Apr '11

Hi all, Does any one have (or galaxy team: are you planning to develop) tools for NCBI's SRA binary container format ? For starters, a wrapper for the "fastq-dump" program that converts a lite-sra back to fastq ? Just trying to avoid re-inverting a wheel, -gordon

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How to control which nodes particular applications run on
by Ryan Golhar 01 Apr '11

01 Apr '11

Hi all - Is it possible to define in a tool's XML file specific nodes in a cluster that the tool should run on? I have a few machines in my cluster is lots of RMA that I need for a specific tool. However there is no way to guarantee the tool will execute on one of those nodes. Is this possible? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt
by Dave Clements 01 Apr '11

01 Apr '11

Hello all, Dan Blankenberg will be giving two workshops on Galaxy at the University of Pittsburgh on April 6. The presentations are open to the public. See below for details and please contact Dan, or Carrie Iwema at Pitt, if you have any questions. Thanks, Dave C. Intro to Galaxy http://galaxy.psu.edu/ Dan Blankenberg, PhD Center for Comparative Genomics & Bioinformatics Penn State University Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples & more... Wednesday 6th April *10 am – 12 pm Intro to Galaxy (general interest) * * * *2 pm - 4 pm Working w/NGS Data (advanced users) * University of Pittsburgh Falk Library Conference Room B You are welcome to bring your laptop. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carrie L. Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh 200 Scaife Hall 3550 Terrace St Pittsburgh, PA 15261 412-383-6887412-648-8819 (fax)iwema(a)pitt.eduwww.hsls.pitt.edu/molbio ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Re: [galaxy-dev] bug 8-bit bytestrings
by Paul-Michael Agapow 01 Apr '11

01 Apr '11

> "ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings > unless you use a text_factory that can interpret 8-bit bytestrings (like > text_factory = str). It is highly recommended that you instead just > switch your application to Unicode strings." I'd hazard that the easiest way to solve this problem is to explicitly encode the url when you pass it to the other program, something like: myprog.pl --use-this-url #echo eightbitstr.encode('utf-8') ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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bug 8-bit bytestrings
by Bataillie Michiel 01 Apr '11

01 Apr '11

Hello galaxy community, I developed a tool for galaxy which runs fine (tool does everything what it's supposed to do) but there's always this error that occurs when the tool has finished it's job. It's seems to be a bug related to python and common for certain python versions (I use python 2.6 for my local instance of Galaxy). This is the error that Galaxy gives when the tool has finished his job: "ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings." One of the inputs of my tool is text (type="text"), a URL(http://...) that needs to be given by the user. This URL is then given to my Perl script and the script runs fine(does everything what it's supposed to do). It seems that python complains about this specific piece of input, python says that the input is a 8-bit bytestring and only unicode (UTF-8) strings should be used in the text input... How can I get around this issue, so that python stops giving me this error? thanks in advance kind regards Bataillie M.

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