Re: [galaxy-dev] is there a simple way to access an arbitrary dataset's absolute path?

Hi Gus Have a look at Shantanu's email from last October: http://dev.list.galaxyproject.org/displaying-dataset-paths-in-the-UI-td4142007.html It works very well for us. Regards, Hans On 04/05/2012 08:46 PM, W. Augustine Dunn III wrote: Hello all: There are times when I want to explore

[galaxy-dev] Using quota won't decrease

Dear Galaxy users, I run a local instance of Galaxy on my university's server and I stumbled upon an issue concerning using quota on the upper right corner of the interface. It says I'm using a certain amount of GBs even though I have deleted all raw data from the /galaxy-dist/database/files d

Re: [galaxy-dev] [galaxy-user] permissions on folder created by Galaxy

Hi Thanks for your answer, and for pointing me to the right mailing list. My tool actually feeds data libraries. It works in a similar way as the "Copy data into Galaxy? No" functionality, in the sense that it creates symbolic links rather than duplicating files, but it also provides an inte

[galaxy-dev] An error occurred running this job: Args must match #! line at /PATHTOGALAXY/galaxy-central-hbc/tools/filters/fixedValueColumn.pl line 1.

Hello, When we try to add a column to a dataset we get the following error: An error occurred running this job: *Args must match #! line at /share/shared/galaxy-central-hbc/tools/filters/fixedValueColumn.pl line 1. * Perl documentation says this; (F) The setuid emulator requires that the argumen

Re: [galaxy-dev] is there a simple way to access an arbitrary dataset's absolute path?

Brilliant! On Tue, Apr 10, 2012 at 1:19 AM, Hans-Rudolf Hotz wrote: > Hi Gus > > > Have a look at Shantanu's email from last October: > > http://dev.list.galaxyproject.**org/displaying-dataset-paths-** > in-the-UI-td4142007.html

[galaxy-dev] Traceback on original execution

Hi, Galaxy, Developers, My name is Dan Sullivan and I work at the University of Chicago in the newly-formed Center for Research Informatics. This is my first post to this list, and I am a very new Galaxy user, so please be patient with me :-) I have a question regarding an error I am reciecveing

Re: [galaxy-dev] Traceback on original execution

On Apr 10, 2012, at 2:42 PM, Daniel Patrick Sullivan wrote: > Is this somthing that somebody could possibly commment on? Should I > just try to install a more recent version of python? Thank-you so > much for your help and guidance. Hi Dan, This past October we did officially deprecate python

Re: [galaxy-dev] Workflow API (runtime modification of tool parameters)

Richard, For specifying or changing species, you may want to inspect the input via the API (api/histories//contents//) and snag the "genome_build" attribute that way. Or am I missing the issue you're running into? As an aside, I'd love to look at the runtime parameter specification changes y

[galaxy-dev] Is there any way to restrict the access of a local Galaxy instance

Dear all, I installed a local Galaxy instance for my company. Different from the regular setting, we want to restrict the access of our local Galaxy instance only to the people in our company, which means it is not open to public. After new configuration, to use the service provided by our Galaxy

[galaxy-dev] Directories in $output.files_path

Hi Galaxy developers, I'm adding a tool to my Galaxy instance which generates some directories in the directory $output.files_path, but when I look in database/files/000/dataset_X_files/ directory, the directories has been copied as an empty plain text files. There is any option in unive