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

Issues displaying/downloading datasets
by Josh Nielsen 18 Jan '12

18 Jan '12

Hello all, I recently have been having problems viewing/displaying datasets (with the eye icon) as well as downloading datasets in Galaxy which I have uploaded, although I can actually point to those datasets as input to other tools and they show up on the drop down menus and it runs perfectly. Every time that I click on the eye icon for a dataset in my history pane I get an apache error which displays in the window that says it cannot find /galaxy/datasets/XXXXX/display/?preview=True. I see a corresponding entry like this in paster.log (for example): *[17/Jan/2012:09:53:03 -0500] "GET /galaxy/datasets/92b83968e0b52980/display/?preview=True HTTP/1.1" 200 - " http://galaxy-dev.haib.org/galaxy/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101 Firefox/8.0.1"* For downloads I get the same error except that the requested URL is: *GET /galaxy/datasets/92b83968e0b52980/display?to_ext=txt* The alphanumeric code is of course different for each dataset but I am puzzled at how to even debug this because I cannot find anywhere on the file system or under the galaxy-dist directory any path that is named "datasets" and has a "display" subfolder (so I assume it is an internal url/path notation). I looked at the python code some and all I got was a headache. I see that it uses a fetch url method to grab a specific url for each dataset but I'm not sure what it is actually looking for on the file system, or if the url is just an alias to something else. I thought to check in the MySQL database but didn't see any corresponding values that matched "datasets" or the alphanumeric code (which I still can't tell where it is getting that from). Everything else in Galaxy works fine except for this. Could anyone please point me in the right direction about how to debug this? It would be much appreciated! Thanks, Josh

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An error occurred...
by Milos Busarcevic 18 Jan '12

18 Jan '12

Hi, I've got this message after trying to run Cufflinks on the Main instance: "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" Is this a global problem and is there a way to fix it? Thanks, Milos

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change in paster.py?
by Ryan Golhar 17 Jan '12

17 Jan '12

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Share some code (xml) to wrap IGV itself as a Galaxy visualizer
by bt.microzhang＠gmail.com 17 Jan '12

17 Jan '12

Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply. Regards, Ming

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rgenetics & galaxy
by Ivan Merelli 17 Jan '12

17 Jan '12

Hi, I'm trying to use rgenetics in galaxy, but I have some problem in installting rpy-1.0.3 with R-2.13.1. I found this guide, which is about the same problem of mine: http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590.html but didn't work for me (although the part about the modulefile is quite obscure for me). The problem seems to be correlated to an header file (Rdevices.h) which is no more present in the latest R distribution. Any hints to solve this problem? May I use rpy2? Best, Ivan

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importing large files into local instance
by Joshua Gross 17 Jan '12

17 Jan '12

Hello all-- We have set up a local version of Galaxy on our own server. On the same computer, we have a couple ~27 GB fastq files we want to use in Galaxy, but we have not figured out how to import them. Since they are on the same HDD, we imagine that there is a way to simply copy them into a folder or something. Is there a simple way to import these files? We have been unable to locate anything in the documentation that directly addresses this issue. Thanks a lot for your time! Josh Gross

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galaxy command line
by Usha Reddy 16 Jan '12

16 Jan '12

Galaxy is a web based platform. Can Galaxy be run as a command line tool? Thanks, Usha

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Getting "global name 'copy_sample_loc_file' is not defined" error when trying to install tool
by Anthonius deBoer 13 Jan '12

13 Jan '12

Im trying to install a tool from the toolshed that showed me this error. NameError: global name 'copy_sample_loc_file' is not defined I know the tool is trying to install the loc file...Does this not work yet? Thon

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tool restrict access
by Ivan Merelli 13 Jan '12

13 Jan '12

Hi, how can I restrict the access of a Galaxy tool to a specific user in an login free instance of Galaxy? I see a suggestion in this post http://gmod.827538.n3.nabble.com/Galaxy-Tool-permission-Access-td3348890.ht… but it's really workround, I was seeking for a cleaner solution... Thanks, Ivan

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Picard MarkDups
by Ryan Golhar 13 Jan '12

13 Jan '12

I'm trying to run Picard MarkDups through Galaxy. Picard is using the standard 4g for the java max heap size. I need to increase this. Is it possible to offer this as an option to the user? If not, where do I change this? I see the entry in picard_wrapper.py. Do I change it here or in the XML file for MarkDups? Ryan

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