galaxy-dev March 2011

galaxy-dev@lists.galaxyproject.org

71 participants
111 discussions

In Europe? Galaxy Team Members will be available for a visit
by Dave Clements 31 Mar '11

31 Mar '11

Hello all, If you have a Galaxy installation and are based in Europe, then please keep reading. The Galaxy Team will be in Europe in late May for the 2011 Galaxy Community Conference (GCC, http://galaxy.psu.edu/gcc2011/). Several team members are available before and/or after the meeting to visit European Galaxy installations to help with installation, configuration and tool integration. There are two important caveats: 1) *We need to hear from you as soon as possible*, and have plans more or less *worked out by the end of Monday, 4 April*. We are planning to buy our plane tickets on Tuesday. 2) *The host institution needs to pay all in-Europe travel costs*, including the cost to get from the Netherlands to your site and back, and lodging and transport costs while at your site. Galaxy will pay to get people to Europe, but you need to get us the rest of the way. Please let me know if you are interested or if you have questions. Thanks, Dave C PS: Early registration (save 20%) for the GCC ends 24 April. http://galaxy.psu.edu/gcc2011/Register.html -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Can't save BAM file from Galaxy
by Liisa Koski 31 Mar '11

31 Mar '11

Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM file. It does not happen when I try to save a txt file. python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l < 2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@ Something to do with base positions? Thanks in advance for any help, Liisa

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extra hack to get own database connection to work?
by Perdacher,Martin 31 Mar '11

31 Mar '11

hello galaxy-community, we stored a lot of peak-information in a database. to import these files into galaxy, i read the DataConnectionProtocol (https://bitbucket.org/galaxy/galaxy-central/wiki/DataSources) and i also took a look at the biomart.xml example (https://bitbucket.org/galaxy/galaxy-dist/src/8729d2e29b02/tools/data_source…). biomart does exactly what i want. here is my full tool configuration xml-file: <tool id="regionDb" name="RegionDb-Import"> <description>Import from regionDb</description> <command interpreter="python">../data_source/data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://localhost:8888/index.html" check_values="false" method="get"> <display>Display-Text</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> <param name="tool_id" type="hidden" value="regionDb" /> </inputs> <request_param_translation> <request_param galaxy_name="URL" remote_name="URL" missing=""/> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> <request_param galaxy_name="name" remote_name="name" missing="Biomart test query" /> </request_param_translation> <outputs> <data name="regionDb File" format="bed" label="regionDb import" /> </outputs> <help> **What it does** import ... </help> </tool> content of http://localhost:8888/index.html: <form method="POST" type="text" action="http://galaxy/tool_runner/regionDb?type=text&name=new%20history%20entry&URL…" > <input type="submit" value="Send to Galaxy"/> </form> i also tried a different action="http://galaxy/tool_runner?tool_id=regionDb&type=text&name=new%20history%20e…" with the same error message (shown below). what actually works is, if i try to receive biomart data with this request. <form method="POST" type="text" action="http://gen43/galaxy/tool_runner/biomart?type=text&name=ne%20history%20entry…" > <input type="submit" value="Send to Galaxy"/> </form> my question is: was there some extra hack to get the biomart tool to run? i found some lines in the lib/galaxy/web/controllers/tool_runner.py which confirm that assumption: #Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back @web.expose def biomart(self, trans, tool_id='biomart', **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd) Server Error URL: http://galaxy/tool_runner/regionDb?type=text&name=new%20history%20entry&URL… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:109 in __call__ >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.controllers.tool_runner:27 in regionDb >> return self.index(trans, tool_id=tool_id, **kwd) Module galaxy.web.controllers.tool_runner:75 in index >> template, vars = tool.handle_input( trans, params.__dict__ ) Module galaxy.tools:933 in handle_input >> _, out_data = self.execute( trans, incoming=params ) Module galaxy.tools:1225 in execute >> return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history ) Module galaxy.tools.actions:291 in execute >> wrap_values( tool.inputs, params ) Module galaxy.tools.actions:154 in wrap_values >> input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) KeyError: 'GALAXY_URL' extra data CGI Variables CONTENT_LENGTH '-1' CONTENT_TYPE 'application/x-www-form-urlencoded' 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=c6ca0ddb55be603af8ffade046cb8ca7fe7a18f326db29b947c846a3b24831e1362e15c491e90b43' HTTP_HOST 'gen43' HTTP_REFERER 'http://localhost:8888/index2.php?GALAXY_URL=http%3A//gen43/galaxy/tool_runn…' HTTP_REMOTE_USER 'perdacher(a)genau.at' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.3) Gecko/20100401 Firefox/3.6.3' HTTP_VIA '1.1 gen43.imp.univie.ac.at' PATH_INFO '/tool_runner/regionDb' QUERY_STRING 'type=text&name=new%20history%20entry&URL=http://localhost:8888/getfile.php' REMOTE_ADDR '10.42.111.27' REQUEST_METHOD 'POST' SCRIPT_NAME '/galaxy' SERVER_NAME 'gen43.imp.univie.ac.at' SERVER_PORT '9191' SERVER_PROTOCOL 'HTTP/1.1' Configuration __file__ '/projects/solexadst/serverData/galaxy-devel/universe_wsgi.webapp.ini' admin_users 'tamir(a)genau.at' apache_xsendfile 'False' brand 'GenAu-Epx Development!!!' cookie_path '/galaxy' debug 'TRUE' enable_api 'True' enable_job_running 'False' enable_pages 'True' here '/projects/solexadst/serverData/galaxy-devel' log_level 'DEBUG' new_user_dataset_access_role_default_private 'True' remote_user_logout_href '/logout' remote_user_maildomain 'genau.at' require_login 'True' set_metadata_externally 'True' static_cache_time '360' static_dir '/projects/solexadst/serverData/galaxy-devel/static/' static_enabled 'True' static_favicon_dir '/projects/solexadst/serverData/galaxy-devel/static/favicon.ico' static_images_dir '/projects/solexadst/serverData/galaxy-devel/static/images' static_scripts_dir '/projects/solexadst/serverData/galaxy-devel/static/scripts/' static_style_dir '/projects/solexadst/serverData/galaxy-devel/static/june_2007_style/blue' upstream_gzip 'False' use_interactive 'False' use_remote_user 'True'

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Alternative to the conditional tag, if-else in XML file?
by Kempenaar, M (med) 31 Mar '11

31 Mar '11

Dear list, For a tool that I'm writing I would like to show or hide certain parameters based on what the user entered in other parameters. Normally I would use the conditional tag combined with a select menu which works fine in most cases. However, I also use a selectbox with the following settings: <param name="report_options" type="select" multiple="True" display="checkboxes" label=".." /> As far as I'm aware, it is impossible to use things like 'refresh_on_change' or making a conditional with it since multiple options can be selected. Optimally what I would like to do is something like this (I know the syntax is incorrect): #if "option1" in $report_options #<param name="new_option1" type="text" /> #else if "option2" in $report_options #<param name="new_option2" type="integer" /> #end if But I tested it and the if/else stuff is ignored by Galaxy, is this due to the fact that the XML code is evaluated first and the Cheetah template only when the 'execute' button is pressed? -- Another few small questions: - When using the (deprecated) <page> tag, can I get a 'Previous' button? - Where can I find instructions on the alternative of the <page> tag ("refresh_on_change")? Thanks in advance. Kind regards, Marcel. ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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MySQL 2 Postgres
by SHAUN WEBB 31 Mar '11

31 Mar '11

We are experiencing issues with workflows where jobs are running before the previous step is completed (especially with large workflows). I am wondering if the problem is MySQL. Does anyone know of a reliable script for converting a MySQL dump to PostgreSQL? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [galaxy-dev] DB access and password field in galaxy
by Bossers, Alex 30 Mar '11

30 Mar '11

Hello all, Maybe I posted it wrong. But below my original message again. Any ideas? Thanks Alex -----Oorspronkelijk bericht----- Van: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: zaterdag 19 maart 2011 10:23 Aan: galaxy-dev(a)lists.bx.psu.edu Onderwerp: [galaxy-dev] DB access and passowrd field Hi All, I have some tools that generate mostly tabular output. The next step is to aggregate the data for complex filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Also in light of some data curation tools we use externally of galaxy. Tools and cmd line wrappers can easily connect to a DB (another database than galaxy is using of course) when providing the details for access like address:port, username and password. Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages. Or is this a bad thing to pursue anyway? Thanks for any directions. Alex

2 2

Wiki bug for updating local galaxy?
by Ryan Golhar 30 Mar '11

30 Mar '11

Hi all - I was about to update my local Galaxy installation, and went back to the wiki to refer to how to do this (https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy), and noticed a mistake. Step 1 says to use "hg clone https://bitbucket.org/galaxy/galaxy-dist/" Step 5 says "If you used the instructions shown on this bitbucket wiki (eg hg clone https://[your id](a)bitbucket.org/galaxy/galaxy-central/ )..." I think it would be better if step 1 was in sync with step 5. How can I resolve the fact that I used Step 1 initially and now want to update my instance of Galaxy? 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 1

workflow representation and execution...
by Kostas Karasavvas 30 Mar '11

30 Mar '11

Hi all! I have two questions: 1) Where are workflows saved in the filesystem? Are they saved as xml files (or something) that describes the structure of the workflow/pipeline? (e.g. tools to run, parameters, etc.) 2) When a cluster is used, does a complete workflow run on one node or is it possible that multiple tools in the same workflow are executed in different nodes? Thank you in advance! Kostas

3 6

Alternative bowtie tools
by Assaf Gordon 30 Mar '11

30 Mar '11

Hello all, We're developing alternative bowtie tools that more closely suit our needs, are we're happy to share (and get comments). The main differences are: 1. separate tools for paired-end and single-end 2. the tools accepts FASTA, FASTQ in both Sanger and Illumina format (no more need for grooming). Illumina is the default for newly uploaded FASTQ files. 3. fewer visible options, only the most relevant ones are available (IMHO better organized) 4. optional output of non-mappers and maxed-out mappers as FASTQ files (to use in downstream analysis or remapping attempts) 5. allows users to to do "quiet" output (only aligned reads are reported in the SAM file). 6. allows users to specify custom options (free text field), for those who know what they are doing. 7. Outputs a sorted SAM file, and sorting is done using multi-threaded sort. You can see the interface (but not run the tools) here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_bowtie_se1 http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_bowtie_pe1 The tools (XML & shell scripts) are available here: http://cancan.cshl.edu/labmembers/gordon/files/galaxy_bowtie_tools.tar.bz2 Note about multithreaded bowtie: currently the tools use 10 threads (hard-coded in the XML files) - easily changeable. Note about the sorting: The "sam_sort.sh" script requires the latest sort from coreutils-8.10 (which does multi-threaded sort). The number of threads, maximum amount of RAM allowed for sort, and temporary storage directory are all hard-coded in the beginning of the script - easily changeable. TopHat and Cufflinks tools will follow soon (if there's any interest). Comments are of course welcomed, these are very much work-in-progress. -gordon

6 11

Sequencer Configuration
by Joe Cruz 29 Mar '11

29 Mar '11

Hello, Where can I find information on setting up Galaxy to communicate directly with a sequencer? I know of this place: http://main.g2.bx.psu.edu/u/rkchak/p/sts-admin-setup-sample-tracking but it doesn't seem to be up to date since there are no Sequencer Configuration options on my Admin page (instead External Services, which only has ABI SOLID 3 type). Your help is very much appreciated. Joe

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galaxy-dev March 2011