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

sample for video for example 3 in ngs analyses in galaxy
by Linda McMahan 26 Oct '11

26 Oct '11

Hi, I am watching the video 'Example 3<http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html> - mapping paired-end Illumina run and visualizing results at UCSC Browser', and would like to try out the exercise. I don't have paired-end Illumina fastq sample, Could you provide me the sample mentioned in the video or point me to the location where I can get a small human paired-end Illumina fastq sample to try out the exercise in example 3. Thanks, Linda McMahan

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updating configuration files after code update
by Andrew Warren 26 Oct '11

26 Oct '11

When first running Galaxy there are a number of files that are created including universe_wsgi.ini. After doing an 'hg pull -u' the sample version of this file will be updated but not the specific server instance of the file that was initially created. I was wondering if there are any other files like this that need to be updated/merged/replaced as development continues? Also, does anyone have any good practices or methods for updating configuration files? (right now I'm just using a visual diff and merge to get the new options for universe_wsgi.ini) Sorry if this has been covered somewhere or asked before, I couldn't find any material on it. Thanks, Andrew Warren

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Sever error while trying to join on genomic intervals
by Bart Pannebakker 26 Oct '11

26 Oct '11

Dear developers, I got the following error on the public server while trying to join to datasets on their genomic intervals: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) I know this is not much information, hope you can help to solve the error. Kind regards, Bart

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Error moving tool-data dir ... bowite indexes missing
by Bossers, Alex 26 Oct '11

26 Oct '11

On our up-to-date galaxy_central version I have successfully moved the database/files directory to mounted storage. After adapting the universe_wsgi.ini it works fine after galaxy restart. Now the tool-data dir becomes bigger and bigger and I wanted to move that to mounted storage as well. I moved the tool-data dir to the other location, made sure file permissions were ok and adapted the universe_wsgi.ini tool_data_path to match the new tool-data location. Galaxy restarts and the loc files are read (since blast recognises its databases). However, the bowtie indexes are not read since they do not show up in the NGS bowtie mapper for illumina..... what could be wrong? When I restore the universe_wsgi.ini it works all fine. I am puzzled. Alex

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BWA wrapper error
by dhivya arasappan 26 Oct '11

26 Oct '11

Hi all, I'm seeing the following error when I try to use the galaxy BWA wrapper for SOLID data : An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found Any suggestions in figuring out what this error has to do with would be appreciated. thanks Dhivya

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BWA mapping error on local install
by Christopher Callaway 26 Oct '11

26 Oct '11

Hi, I have Galaxy running locally and when trying to BWA map a set of paired-end reads, the reference genome does not show up (mm9) by selecting either History or Built-in. How do I fix this? Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way #2222 Salt Lake City, UT 84108

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displaying dataset paths in the UI
by Shantanu Pavgi 26 Oct '11

26 Oct '11

I am trying to display dataset paths in the UI when user clicks on the 'view details' icon in the history panel. I was able to display it by adding 'hda.file_name' field in the show_params.mako template file and it seems to be working. Following is a diff for it: {{{ diff --git a/templates/show_params.mako b/templates/show_params.mako index 9f7ad36..58d8108 100644 --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -50,6 +50,8 @@ <tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr> <tr><td>Format:</td><td>${hda.ext}</td></tr> <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr> + <tr><td>Dataset ID:</td><td>${hda.dataset_id}</td></tr> + <tr><td>Dataset Path:</td><td>${hda.file_name}</td></tr> </table> <br /> <table class="tabletip"> }}} It doesn't display any metadata files associated with the dataset. I guess it will need some more changes in the datasets controller to return metadata file paths to this template. But, are these right places to make changes for displaying dataset paths or are there any other files/modules that should be modified? Any comments or suggestions for implementing this will be really helpful. -- Thanks, Shantanu.

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Printing when catching exception get stuck
by Timothy Wu 26 Oct '11

26 Oct '11

Hi, I wrote a Python program which prints something to stdout while catching an exception handling. The code works fine running it standalone. However, when run under Galaxy the code appears to stuck in that printing statement. (At least, as far as I could tell through logging via the logging module). It doesn't actually always gets stuck there since my program run into it multiple times. It enters and exists several times before during the same execution of the program. However, it does always stuck in a particular entry into that exception. Does anyone have a similar experience? I have no idea why that is so. Logging what's printed to stdout to the file encounters zero problem. Timothy

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October 25, 2011 Galaxy Development News Brief
by Jennifer Jackson 25 Oct '11

25 Oct '11

October 25, 2011 Galaxy Development News Brief This release: http://galaxyproject.org/wiki/News%20Briefs/2011_10_25 Release history: http://galaxyproject.org/wiki/News%20Briefs Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 338ead4737ba Highlights: Galaxy is Hiring! Main Data and Job Quotas UI Updates Trackster (GTB) at BioVis Python 2.4 -> 2.7 Official SICER, Trinity, SAMtools rmdup All: What's New Galaxy Main User Interface (UI) Trackster (Galaxy Track Browser) Python and OS Support Galaxy Tool Shed Updated & Improved Tools Quotas and Data Management Source API Scripts Bug Fixes Thanks for using Galaxy!

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Error in using Palmapper
by Fayyaz ul Amir Afsar Minhas 25 Oct '11

25 Oct '11

Hello all, I am using Galaxy to align short reads of length 75 from A. Thaliana (TAIR 9.0) with Palmapper. However, I get the following error: *splice site position (366706) greater than chromosome length (154478)* Can anyone help me in this? Best, -Fayyaz

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