April 2011 - galaxy-dev - lists.galaxyproject.org

Optimizing Disk space using by combining mapping with SAM-to-BAM
by Ryan Golhar 05 Apr '11

05 Apr '11

Hi all - I find it redundant to hold on to SAM output from NGS Mapping tools such when I end up converting the SAM files to BAM files anyway. The cleanup scripts require the history items to be deleted, but I don't want to delete them yet as I want the entire workflow to be kept until we are done analyzing our data. So, I was thinking of a way to remove the intermediate SAM files and thought how I would do this on the command line...simply pipe the output of BWA to samtools to create a BAM file and never have a SAM file to deal with. The BWA tool runner can be modified to pipe BWA output directly to samtools so a SAM file is never physical stored on disk. Has anyone done this? Does this seem like a good idea? Ryan -- 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.

2 2

Missing Page Editor Components
by Charlis Hsia 05 Apr '11

05 Apr '11

Hi all, Wonder if I can get some help from here for the following questions: I just pulled the galaxy-central and installed it. It runs fine. However, when I tried to use the Edit Pages function, there is no "Embed Galaxy Object" and "Insert Link to Galaxy Object" in the "Page Editor". I have set the "enable_pages = True" in "universe_wsgi.ini". Wonder what else can cause the problem? Also, is there any documentations for the control syntax used in datatypes and tools configure xmls? Thanks! Charlie

3 3

Updating BLAST+ wrapper
by Peter Cock 05 Apr '11

05 Apr '11

Hi all, The NCBI have just released BLAST 2.2.25+ which includes some interesting new stuff of interest to the tabular output, i.e. "Added support for query and subject length to tabular output" I would therefore like to update my BLAST+ wrappers in Galaxy to add these two columns to the 'extended tabular' output option. They are going to be very helpful as you can now calculate things like the percentage identity (or similarity) compared to the query or sequence. If there are no objections I propose to add these as columns 23 and 24 (i.e. at the end), so minimise disruption to anyone already using the tabular output. I would hope to have a branch ready for merging next week... Peter

2 14

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

1 1

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

1 1

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

3 4

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

2 1

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

2 1

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

3 3

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.

2 1