March 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Data source tool doesn't source data
by Mark Johnson 26 Mar '12

26 Mar '12

Looks like I'll have to try again. Maybe with a more general question (?) When you're debugging tools, how do you get Galaxy to tell you what the tool is doing? My tool doesn't work properly, but paster.log just shows a line for the request. It doesn't say anything about what tool_runner is trying to do. In short, how do you debug tools? Thanks --Mark Johnson NCBI

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Using direct upload (as SRA/ENA) in our own instance
by Haarst, Jan van 26 Mar '12

26 Mar '12

Dear All, If i browse (outsode of Galaxy) to e.g. http://www.ebi.ac.uk/ena/data/view/SRP001343 , and click on the "Galaxy" links on that page, it used to be that the file got uploaded to my section of the public Galaxy instance. This was probably a bug instead of a feature, as currently it doesn't work anymore. When it did work, it was really handy, and I wondered whether there is a way I could get this working in our own instance, as an easy way to get data into our Galaxy instance outside of Galaxy. This would save users copying the URLs of data to the "Upload File" form. -- Jan van Haarst Assistant Researcher Bioinformatics Wageningen UR, Plant Research International Applied Bioinformatics P.O Box 167, 6700 AD, Wageningen, the Netherlands Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands ++31-317480756 msn:jan.vanhaarst@wur.nl www.pri.wur.nl<http://www.pri.wur.nl/> www.appliedbioinformatics.wur.nl<http://www.appliedbioinformatics.wur.nl/> www.disclaimer-uk.wur.nl<http://www.disclaimer-uk.wur.nl/>

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dotmatcher error
by Sivasangari NANDY 26 Mar '12

26 Mar '12

Hi everyone, A little problem with the dotmatcher tool in Galaxy from Emboss.I've got this message : Tool execution generated the following error message:Devices allowed (with alternative names) are:- ps (postscript) hpgl hp7470 hp7580 meta cps (colourps) tek (tek4107t) tekt (tektronics) none (null, text) data svg Error: Invalid graph value 'png' Died: dotpath terminated: Bad value for '-graph' with -auto defined And one more question : Are we able to move on the "png" graph generated by this tool or is it just a static picture? Advance thanks friends, Siva

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Galaxy SNPEff Display Bug (2nd Independent Report)
by John David Osborne 26 Mar '12

26 Mar '12

Hi Pablo, About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy – we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418 The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable. I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken too…. -John

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refresh_on_change is broken?
by Leandro Hermida 23 Mar '12

23 Mar '12

Hello, Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem? regards, Leandro

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Data source tool doesn't source data
by Mark Johnson 23 Mar '12

23 Mar '12

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Update on Megablast?
by Luobin Yang 23 Mar '12

23 Mar '12

Hi, all, Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy? Thanks, Luobin

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Reference genomes at local instance of Galaxy
by Yang, Yanming 23 Mar '12

23 Mar '12

Hi, I have just installed a Galaxy instance at my local machine and uploaded some sequence data into it. But, when I tried to some NGS tools which need reference genome, i found the selection window was empty. I wonder how to get a reference genome data (e.g., hg19) incorporated into the local Galaxy. Any help will be greatly appreciated. Thanks! Yanming

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Galaxy AMQP listener startup script error
by Leandro Hermida 23 Mar '12

23 Mar '12

Dear all, I followed the directions in https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer to set up the Galaxy AMQP listener service so that the sample tracking system can transfer datasets. When running nohup sh run_galaxy_listener.sh & Traceback (most recent call last): File "scripts/galaxy_messaging/server/amqp_consumer.py", line 33, in <module> from galaxy.web.api.requests import RequestsAPIController File "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/web/api/requests.py", line 7, in <module> from galaxy.web.base.controller import * File "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/web/base/controller.py", line 17, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/visualization/tracks/data_providers.py", line 11, in <module> pkg_resources.require( "pysam" ) File "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/eggs/__init__.py", line 415, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['pysam'] But Galaxy runs fine and the pysam eggs are already there for a long time as they are used by Galaxy. What could be the problem? kind regards, Leandro

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Allow dataset with custom build to be displayed in local IGV
by Sarah Diehl 23 Mar '12

23 Mar '12

Hi all, is there some way I can allow datasets (specifically bam files) that are annotated with a custom build to be displayed in a local IGV (assuming a genome with the same name was generated for IGV)? I tried some things with display_applications/igv/bam.xml, but I couldn't get it to work properly. One challenge is to disable the filter for the local igv and the second challenge is to not do the build name mapping for custom builds. Here is what I tried, but didn't work (filter is still applied to local IGV): <filter> #if $site_id.startswith( 'local_' ) ${dataset.dbkey in $site_dbkeys} #end if </filter> <param type="template" name="site_organism" strip="True" > #if $bam_file.dbkey in $site_dbkeys $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] #else $bam_file.dbkey #end if </param> Any help is greatly appreciated! Best regards, Sarah

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