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

Galaxy version / Mercurial
by Sarah Maman 09 May '12

09 May '12

Hello, I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ? The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version. Thanks a lot, Sarah Maman

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MPileup reference genome bug?
by Lucy A. Skrabanek 08 May '12

08 May '12

I am generating a pileup of BAM data from the 1000 genomes project using MPileup. I have associated the BAM file with the hg19 genome, but every single reference base in the output appears as an N. Is there some extra step I have to perform when using a BAM file that was not generated from within Galaxy? Many thanks, luce

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Fill in parameters via URL
by Kyle Ellrott 08 May '12

08 May '12

Is there a way in Galaxy to provide a link to a tool that fills in some of the parameters? The example is like the URL for GenePattern: http://genepattern.soe.ucsc.edu/gp/pages/index.jsf?lsid=PreprocessDataset&i… When the user clicks the link, it opens up the PreprocessDataset tool with input.filename set to the URL of the file. I'd like to do the same with a workflow, something that downloads the file and then runs a set of tools. Is that possible? Kyle Ellrott

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[Fwd: Tracking .bai files]
by Unknown 08 May '12

08 May '12

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[Fwd: SAM to BAM tool for custom genome build]
by Unknown 08 May '12

08 May '12

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update problem
by Frank Sørensen 08 May '12

08 May '12

Hi Guys, After the most recent 'hg pull -u' followed by 'hg merge', I get the following error in paster.log when I try to restart Galaxy: galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,375 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,376 Loaded history import tool: __IMPORT_HISTORY__ Traceback (most recent call last): File "/usr/local/bin/moma/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/bin/moma/galaxy/galaxy-dist/lib/galaxy/app.py", line 129, in __init__ self.job_manager = manager.JobManager( self ) File "/usr/local/bin/moma/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 30, in __init__ if self.app.config.server_name in self.app.config.job_handlers: AttributeError: 'Configuration' object has no attribute 'server_name' What am I doing wrong? Is there another way to update, when I don't want to loose my own changes - actually additions as in new tools ans tool xml-files? When I run 'hg merge' I get vim showing me a bunch of changed files. I don't actually know what to do with them, so I just exit vim by :q! until I've been through all the files. Any ideas? Kind regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363

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Migrate history & datasets to new database
by Josh Nielsen 08 May '12

08 May '12

Hello all, I recently tried moving from a tarball install of Galaxy to a Mercurial managed one, and in the process something went wrong with the database upgrade. I had intended to install the Mercurial-based Galaxy separately (though on the same machine) and then move it to production once it was working but it installed in-place over the current database while it was still completely active/up and running. That broke my existing Galaxy install and I had to move to the new install immediately. I recall having to run the Mercurial install's run.sh script multiple times though because the upgrade sequence (looked like 87->88, 88->89, etc. as it progressed) did not complete all the way the first time. I also ran it as root when I probably should have done it as our galaxy user. Long story short now I cannot log in to Galaxy even though Galaxy recognizes correct credentials from the database. My debugging so far has not yielded any results. At this point after a week of unsuccessful attempts to repair the existing install I just want to create a fresh database and migrate over our users' history and dataset (and possibly login credentials) information stored in the database to the new one, if at all possible. Could someone give me any guidance as to how to do that, and which table files (MYI, MYD, etc.) that I should copy over into the new mysql database to make that happen? P.S. I do have to thank Dannon Baker for helping me so far through private email correspondence to try to figure out what went wrong with the current install. However I'm not having any breakthroughs and our local Galaxy mirror has been down for over a week now and I just want to start fresh and migrate over critical data if possible. Thanks for your help, Josh Nielsen

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Using output from prior step to pre-populate text area. Batch download multiple SRA files
by Dave Lin 07 May '12

07 May '12

I'm trying to create a tool for scientists to BATCH download multiple fastq files from EBI based on starting list of SRA-ID's. The EBI-SRA tool seems to only take one ID at a time. Proposed approach: Defin workflow with two steps. Step1: Get list of ID's from user. Lookup FTP/URL for each ID. Step2: Batch download the URL's using a copy of the "upload file" workflow step. I'm trying to prepopulate the "URL/Text" box with the list of FTP-URLS from step 1. This way the user doesn't have to cut/paste text from Step #1. I found the thead on the undocumented dynamic_options functionality. However, not sure that will help here. Question/Discussion 1) Would appreciate any pointers/examples on how to pre-populate the text area of a workflow input step based on the output from a prior step. 2) This approach seems hacky, so would also love to hear suggestions on a better approach. Thanks in advance, Dave

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send data error
by Le-Shin Wu 07 May '12

07 May '12

Hi, We just installed a galaxy server and are doing the tools testing right now. When we were testing the "Send Data" tool, we encountered an error as below. Error executing tool: 302 Found The resource was found at /tool_runner/redirect?redirect_url=http%3A%2F%2Fepigraph.mpi-inf.mpg.de%2FWebGRAPH_Public_Test%2Ffaces%2FDataImport.jsp%3FDATA_URL%3Dhttps%3A%2F%2Fgalaxy.indiana.edu%2Fdatasets%2F6%2Fdisplay%26INFO%3D%26GENOME%3Dhg18%26NAME%3DConvert+genome+coordinates+on+data+4+%5B+UNMAPPED+COORDINATES+%5D%26USERNAME%3Dlewu%40indiana.edu%26GALAXY_URL%3Dhttps%3A%2F%2Fgalaxy.indiana.edu%2Ftool_runner%3Ftool_id%3Depigraph_import Does this mean the redirect URL is wrong or something else? Can someone help us to solve this problem? Thanks a lot. Best LW

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Re: [galaxy-dev] refresh_on_change is broken?
by Kempenaar, M (med) 07 May '12

07 May '12

Hi, The Extract GFF Features doesn't use dynamic options and I don't think that's really the question here. Let me give an example of something that I do. I have the user select a file after which I, using dynamic_options, extract the column names and present those to the user with a select input parameter. With the selected column name I then present a new select input parameter with all the unique values of the selected column. To get this to work I am now using three pages since it is really dynamic, thus after each parameter (that uses dynamic_options) I need to make a new page to use the selected item, thus: <page> <param name="input_dataset" type="data" format="tabular, txt" label="Input dataset" /> </page> <page> <param name="colfilter" type="select" multiple="False" label="Select Filtering Column" dynamic_options="get_columns( input_dataset )" /> </page> <page> <param name="filter_values" type="select" multiple="True" label="Select Filtering Values" dynamic_options="get_filter( input_dataset, colfilter, 2 )" /> </page> .... This works fine, however it requires three pages which is deprecated. The documentation says 'use refresh_on_change' which is an undocumented feature (please (please!!) fix this!) with no examples anywhere on how to replace common <page> usage. So given above example (which is similar to what the original requester asked), where to place the refresh_on_change option to get it working? I've of course tried to place it within both dynamic_option parameters but this doesn't update the 'filter_values' parameter depending on the 'colfilter' parameter.. Kind regards, Marcel http://lists.bx.psu.edu/ </quote> Quoted from: http://gmod.827538.n3.nabble.com/refresh-on-change-is-broken-tp3786745p3852… ------------------------------ Message: 12 Date: Fri, 23 Mar 2012 18:41:11 -0400 From: Jeremy Goecks <jeremy.goecks(a)emory.edu> To: Greg Von Kuster <greg(a)bx.psu.edu> Cc: "Gubian, Sylvain" <Sylvain.Gubian(a)pmi.com>, Galaxy Dev <galaxy-dev(a)bx.psu.edu> Subject: Re: [galaxy-dev] refresh_on_change is broken? Message-ID: <302260D0-F8B3-4C09-AD59-AEB6239C8FC3(a)emory.edu> Content-Type: text/plain; charset="us-ascii" A final pointer: to see tools that use dynamic options, take a look at "Extract GFF features" and "Filter GFF dataset by feature count" Good luck, J. ________________________________ 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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