[galaxy-dev] extra hack to get own database connection to work?
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.xml). biomart does exactly what i want. here is my full tool configuration xml-file: tool id=regionDb name=RegionDb-Import descriptionImport from regionDb/description command interpreter=python../data_source/data_source.py $output $__app__.config.output_size_limit/command inputs action=http://localhost:/index.html; check_values=false method=get displayDisplay-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:/index.html: form method=POST type=text action=http://galaxy/tool_runner/regionDb?type=textname=new%20history%20entryURL=http://localhost:/getfile.php; input type=submit value=Send to Galaxy/ /form i also tried a different action=http://galaxy/tool_runner?tool_id=regionDbtype=textname=new%20history%20entryURL=http://localhost:/getfile.php; 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=textname=ne%20history%20entryURL=http://www.biomart.org/biomart/martview/4905f90905e8f4b362a96b887cc7c452?do_export=1resultsButton=1; 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=textname=new%20history%20entryURL=http://localhost:/getfile.php 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:/index2.php?GALAXY_URL=http%3A//gen43/galaxy/tool_runnertool_id=regionDb' HTTP_REMOTE_USER'perdac...@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
Re: [galaxy-dev] MySQL 2 Postgres
Hi, It's built into mysqldump, just add the following option to your mysqldump command: --compatible=postgresql -Leandro On Wed, Mar 30, 2011 at 3:20 PM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote: 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. ___ 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/ ___ 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/
[galaxy-dev] Alternative to the conditional tag, if-else in XML file?
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. ___ 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/
[galaxy-dev] galaxy related
if i want some in information from tool xml file to code file ,how i will get the info. it it's possible ,send me detailed info. Regards galaxy user shashi shekhar ___ 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/
Re: [galaxy-dev] extra hack to get own database connection to work?
Hi Martin, You uncovered a bug with using check_values=false and tool output labels. A fix was committed in 5289:b453988dce62; thanks for reporting the error. However, there are a couple of issues with your datasource tool configuration -- the most important being the setting of the tool_type and making sure that the output dataset name matches the name that will be used on the command line. I have included some untested alternatives for you below. Please let us know if we can provide additional assistance. Your xml should be similar to these (untested): using latest code: tool id=regionDb name=RegionDb-Import tool_type=data_source descriptionImport from regionDb/description command interpreter=python../data_source/data_source.py $output $__app__.config.output_size_limit/command inputs action=http://localhost:/index.html; check_values=false method=get displayDisplay-Text/display /inputs request_param_translation request_param galaxy_name=data_type remote_name=data_type missing=bed/ /request_param_translation outputs data name=output format=bed label=regionDb import / /outputs help **What it does** import ... /help /tool before fix: tool id=regionDb name=RegionDb-Import tool_type=data_source descriptionImport from regionDb/description command interpreter=python../data_source/data_source.py $output $__app__.config.output_size_limit/command inputs action=http://localhost:/index.html; check_values=false method=get displayDisplay-Text/display /inputs request_param_translation request_param galaxy_name=data_type remote_name=data_type missing=bed/ request_param galaxy_name=name remote_name=name missing=regionDb import / /request_param_translation outputs data name=output format=bed / /outputs help **What it does** import ... /help /tool Thanks for using Galaxy, Dan On Mar 31, 2011, at 4:10 AM, Perdacher,Martin wrote: 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.xml). biomart does exactly what i want. here is my full tool configuration xml-file: tool id=regionDb name=RegionDb-Import descriptionImport from regionDb/description command interpreter=python../data_source/data_source.py $output $__app__.config.output_size_limit/command inputs action=http://localhost:/index.html; check_values=false method=get displayDisplay-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:/index.html: form method=POST type=text action=http://galaxy/tool_runner/regionDb?type=textname=new%20history%20entryURL=http://localhost:/getfile.php; input type=submit value=Send to Galaxy/ /form i also tried a different action=http://galaxy/tool_runner?tool_id=regionDbtype=textname=new%20history%20entryURL=http://localhost:/getfile.php; 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=textname=ne%20history%20entryURL=http://www.biomart.org/biomart/martview/4905f90905e8f4b362a96b887cc7c452?do_export=1resultsButton=1; 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=textname=new%20history%20entryURL=http://localhost:/getfile.php 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
Re: [galaxy-dev] Can't save BAM file from Galaxy
Ryan Golhar wrote: Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off? I'm running into this same problem but still prefer to have the job scripts kept in case something goes wrong. Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd be a simple change, though. Ryan ___ 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/
[galaxy-dev] Updating BLAST+ wrapper
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 ___ 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/
[galaxy-dev] In Europe? Galaxy Team Members will be available for a visit
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/ ___ 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/
[galaxy-dev] Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt
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 pmIntro to Galaxy (general interest) * * * *2 pm - 4 pmWorking 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)iw...@pitt.eduwww.hsls.pitt.edu/molbio -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ 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/
