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

wrong static image URL when clicking re-run
by Assaf Gordon 01 Aug '11

01 Aug '11

Hi, A small bug: When clicking "re-run" to view a tool form, and the tool has embedded images, the URL of the images is not working. When viewing a tool that has embedded images, the relative <img> URL is "./static/images/histogram2.png". The tool's URL comes from: "http://main.g2.bx.psu.edu/tool_runner?tool_id=histogram_rpy" and so the absolute image URL becomes: "http://main.g2.bx.psu.edu/./static/images/histogram2.png" which works OK. But when viewing a tool by clicking "re-run", the tool's URL is: "http://main.g2.bx.psu.edu/galaxy/tool_runner/rerun?id=56" ("rerun" being a method in the "tool_runner" controller), which in turns makes the image absolute URL: "http://main.g2.bx.psu.edu/tool_runner/./static/images/XXXXX.png" - and it doesn't work. Note that the solution of changing all the images URLs in the XML files to start at the root (e.g. "/static/images/XXXX.png") is not optimal, because it will bypass the "prefix" URL that some people use (e.g. with "http://rave.cshl.edu/galaxy" instead of "http://rave.cshl.edu/"). a workaround (when using apache) is to add the following rewrite_rule: RewriteRule ^/tool_runner/static/(.*) /localdata1/galaxy/galaxy_prod/static/$1 [L] Or if using a "/galaxy" prefix: RewriteRule ^/galaxy/tool_runner/static/(.*) /localdata1/galaxy/galaxy_prod/static/$1 [L] -gordon

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GALAXY-GBROWSE : setting up incoming/outcomming functionalities (sharing data)
by BM 01 Aug '11

01 Aug '11

Hi, I am trying to set up the galaxy outgoing and incoming funtionalities in GBROWSE and GALAXY to send data between these applications. I have local instances of GALAXY and GBROWSE and I wonder how should I configure these. How this should look in the GBROWSE user interface (in the "share this track" section) ? How this should look in the GALAXY user interface ? My GBROWSE version : 2.38 and my GALAXY version : galaxy-galaxy-central-fd3391bcd903 Here the conf I set up : ------MY GALAXY SETTINGS------ I saw in a previous topic posted by nicki (http://gmod.827538.n3.nabble.com/Send-data-to-GBrowse-td2446346.html) that some files must be edtited : 1. universe_wsgi.ini I edited it as follows : GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd,perso 2. tool-data/shared/gbrowse/gbrowse_build_sites.txt I edited it as follows : #perso perso http://my_host.com/Gbrowse/cgi-bin/gbrowse_details/specie specie 3. datatypes_conf.xml I edited it as follows :  <display file="gbrowse/gbrowse_gff.xml" inherit="True" />  <display file="gbrowse/gbrowse_wig.xml" /> I have got the following files in "display_applications/gbrowse/" : gbrowse_gff.xml gbrowse_interval_as_bed.xml gbrowse_wig.xml ------MY GBROWSE SETTINGS------ I have edited the general section of "/var/www/GBROWSE/conf/specie.conf" according to the documentation http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options: [GENERAL] galaxy outgoing = http:/my_host.com:8080/tool_runner?tool_id=ncbi_blastn_wrapper galaxy incoming = https://my_host.com/Gbrowse/cgi-bin/gbgff ------------- First, I would like to look for the outgoing functionality from GBROWSE to GALAXY. Then, the incoming functionnality : from GALAXY to GBROWSE I hope someone can help me, I'm new to GALAXY. Thanks, greetings Ben

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use remote data without duplication
by Caroline Prenoveau 19 Jul '11

19 Jul '11

Hi, We are a small lab and we would like to use galaxy to do our analysis. However we have a very large amount of data that is stored on several machines and that we cannot afford to duplicate. Our galaxy server is set up on a different machine. We are looking for a way to use our remote data inside galaxy without copying it locally. Any ideas/hints? Thanks, Caroline

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removing "Select All" / "Unselect All" buttons from a set of check boxes
by Hans-Rudolf Hotz 13 Jul '11

13 Jul '11

Hi Is there a way to remove the "Select All" and "Unselect All" buttons from a set of check boxes? - crated with: <param name="samples" type="select" display="checkboxes" multiple="true" dynamic_options="ds_samplesFromServer()"/> I have a very long list, and I don't want to encourage people to tick all boxes. Thank you very much for your help, Hans

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Re: [galaxy-dev] LAJ Error
by Ellul Jason 13 Jul '11

13 Jul '11

Hi All, I have been able to workaround the problem I was having by modifying the LAJ_code.py to include 'and data != None' on each of the elif statements. i.e. if name == "maf_input": params["alignfile1"] = "display?id=%s" % data.id elif name == "seq_file1" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq1"] = "display?id=%s" % data.id elif name == "seq_file2" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq2"] = "display?id=%s" % data.id elif name == "exonfile" and data != None and data.state == data.states.OK and data.has_data(): params["exonfile"] = "display?id=%s" % data.id elif name == "repeatfile" and data != None and data.state == data.states.OK and data.has_data(): params["repeatfile"] = "display?id=%s" % data.id elif name == "annotationfile" and data != None and data.state == data.states.OK and data.has_data(): params["annotationfile"] = "display?id=%s" % data.id elif name == "underlayfile" and data != None and data.state == data.states.OK and data.has_data(): params["underlayfile"] = "display?id=%s" % data.id elif name == "highlightfile" and data != None and data.state == data.states.OK and data.has_data(): params["highlightfile"] = "display?id=%s" % data.id For some reason, even though repeatfile is optional the script always thinks that a file has been selected, even when one has not. Hence data is equal to None and it throws a 'nonetype has no attribute state' error when it checks data.state==data.states.OK. Could a developer please look into why it would think a file for the option repeatfile had been selected when one hasn't. Cheers, -- Jason Ellul Bioinformatician Cancer Research Division Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.ellul(a)petermac.org Address: St Andrew's Place East Melbourne Victoria 3002 Australia Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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how to purge histories/datasets not accessed/updated for a certain time
by Chaolin Zhang 13 Jul '11

13 Jul '11

Hi, We have a local mirror of the galaxy system and the disk is occupied really quickly. Is there a way to purge histories/datasets not accessed/updated for a certain period of time, no matter if they are deleted by the user? It looks like the current scripts for clean up only purges deleted histories/datasets. Thanks! Chaolin

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plotting/statistics tools suggestion
by Marshall Hampton 12 Jul '11

12 Jul '11

I've just started seriously looking at Galaxy, and I already have a suggestion (everyone's a critic...): switch from using rpy or even rpy2 to scipy/numpy/matplotlib for basic statistics and plots. I wrestled a bit with getting rpy to work on my local setup and decided it would be quicker to write my own plotting tool extensions, which indeed turned out to be the case. Since you already require python it seems much more natural to use python-native tools. To give some positive feedback, learning to write an extension was surprisingly easy and encourages me to work on more. I use currently use Sage (http://www.sagemath.org/) to both analyze next-generation sequence data (454 and Illumina) and create interactive tools for the biologists I collaborate with. The Sage project involves many of the same issues and challenges facing Galaxy. Sage is based on python, but includes R. I realize that there are many things you would want to do with R that aren't included in scipy/biopython, so it might be worthwhile to look at how Sage wraps R. Its far from perfect, but I prefer it to rpy2. In the Sage source tree the interface is at: $SAGE_ROOT/devel/sage/sage/interfaces/r.py. (Ugly online copy at: http://hg.sagemath.org/sage-main/file/361a4ad7d52c/sage/interfaces/r.py) -Marshall Hampton Department of Mathematics and Statistics and the Integrated Biosciences Program University of Minnesota Duluth

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How to download data from History
by colin molter 12 Jul '11

12 Jul '11

Hello all, I have two related questions about getting data from the Galaxy History. I installed `galaxy in my server, I did some data analyses and now i want the resulting data back. But I am facing two problems: 1/ I just try to use the download button. If i do it with the button (or with curl or wget), i get the following error: <h1>Proxy Error</h1> <p>The proxy server received an invalid response from an upstream server.<br /> The proxy server could not handle the request <em><a href="/galaxy/datasets/b701da857886499b/display">GET /galaxy/datasets/b701da857886499b/display</a></em>.<p> Reason: <strong>Error reading from remote server</strong></p></p> </body></html> any ideas? Does I am suppose to modify the universe_wsgi.ini? 2/ In fact, i would prefer to just copy the result on the same server (no need to use the network). Something similar that what is used to add data to the datalibrary. Is it a way to just copy data from within galaxy to some given place in the same server? thank you colin -- Colin Molter University of Brussels - InSilico Team - http://insilico.ulb.ac.be/

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problems with 'Profile Annotations' tool UI
by Hans-Rudolf Hotz 08 Jul '11

08 Jul '11

Hi we are looking into different methods to display dynamic contents in the tool user interface. To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We turned it on in a local installation (May 20, "8c11dd28a3cf" release), but we struggled to get the interface to work. On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is a history item with: "format: bed, database: hg18". But in our local test installation, we don't get the list of tables, no matter whether we have a ('hg18') bed file in our history or not. It looks like as if the 'from_file="annotation_profiler_options.xml"' statement in the "annotation_profiler.xml" is ignored. I know, the file 'annotation_profiler_options.xml' is read, since I get an error during restart, if I provide invalid xml. Is there anything else, I have to enable, in order to get this interface to work? Currently, I don't care about the tools functionality, I just want the (cool) interface to work. Thank you very much for your help. Regards, Hans PS: this question is connected to Tim's question yesterday - I just should have sent mine first - sorry.

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Error when viewing data in GeneTrack
by Lewis, Brian Andrew 07 Jul '11

07 Jul '11

I'm seeing the following error in the log when clicking on the "View in GeneTrack" link for a specific dataset: Error - <type 'exceptions.Exception'>: A data display parameter is in the error state: genetrack_file URL: http://localhost:8081/galaxy/display_application/cbbbf59e8f08c98c/genetrack… File '/usr/local/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/usr/local/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 607 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) File '/usr/local/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 176 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) File '/usr/local/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 116 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) File '/usr/local/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 57 in build_parameter_dict if param.ready( other_values ): File '/usr/local/galaxy-dist/lib/galaxy/datatypes/display_applications/parameters.py', line 120 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file This is happening on a local instance of Galaxy, which has been updated to the most recent revision. Before updating The specific data came from the UCSC table browser. ~ Brian

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