Re: [galaxy-dev] universe_wsgi.ini

Hello Daniel, I had similar issues when setting up our own. The POST size limit is not set by Galaxy. If I remember correctly it's in your Apache config, though I don't remember exactly where it was. For the .loc files, here is an example: dm3-btdm3D.melanogaster 3 /path/to/index

Re: [galaxy-dev] Running galaxy in a cluster as if it was local

> > Is there any way I can set up the PYTHONPATH or other environment > variables so that this would work in the compute node? Try using your galaxy_user's ~/.sge_request file. See http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies for more information. Good luck, J. _

Re: [galaxy-dev] R scripts for DESeq

Just set up the email alert. Thanks. Lisa On Wed, Feb 22, 2012 at 9:27 PM, Greg Von Kuster wrote: > Lisa, > > In case you aren't aware, you can set your user preferences for your account > in the tool shed to receive an email message when a new repository's first > upload occurs.  This would ke

[galaxy-dev] babel egg: epiphany locale setting fix

Dear list, I encountered problems when using galaxy with ubuntu's epiphany browser. It seems that when using this browser, HTTP_ENVIRON's locale setting is sometimes 'en-us', but sometimes ' en-us'. That's a whitespace before the locale. I solved the problem by adding a simple .strip() in egg

[galaxy-dev] How to get raw file name of the uploaded dataset

Dear all, May I ask how to get the raw file name of the uploaded dataset? The value of $input assigned from is a file name like "dist-path/database/files/000/dataset_12.dat". However, I really need to get the raw file name like "abc.xml" which seems to be stored as attribute "name" of the uploade

[galaxy-dev] KeyError: 'datatypes_config'

Hi all, I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory

[galaxy-dev] corrupted binary file

Dear all, I found one of my binary files was corrupted after its uploading through "Get data'. I used editplus to check its hex code and found some "0D" is changed to "0A" and also one byte is lost. May I ask how to solve this problem? Thank you for your help. Best Regards, HU Yingwei __

Re: [galaxy-dev] KeyError: 'datatypes_config'

Hello Sarah, This is due to a known bug (not yet fixed in the distribution). The bug causes the file named "datatypes_conf.xml" included in installed repositories to be deleted. You'll need to go to the directory on disk where your emboss_datatypes repository is installed ( make sure you are

Re: [galaxy-dev] corrupted binary file

On Fri, Feb 24, 2012 at 4:03 PM, Yingwei HU wrote: > Dear all, > > I found one of my binary files was corrupted after its uploading through > "Get data'. I used editplus to check its hex code and found some "0D" is > changed to "0A" and also one byte is lost. May I ask how to solve this > problem?

Re: [galaxy-dev] KeyError: 'datatypes_config'

Hi Greg, thanks for the help! However, the error still persists. I tried to play around with lots of things, but nothing seems to change the error. Sarah On 02/24/2012 05:06 PM, Greg Von Kuster wrote: Hello Sarah, This is due to a known bug (not yet fixed in the distribution). The bug cau

[galaxy-dev] unsubscrb

___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-dev] universe_wsgi.ini

Hi L-A, Thank you for the reply. Another kind member (thanks Dan Dorset!) also took the time to explain me these over the phone this morning. The missing piece of information, which you have included in your instructions, and which was omitted in the documentation, is the link between the bowt

[galaxy-dev] Issues importing a shared workflow

I have a Galaxy user who has created a workflow from a history and share it with me. However, when I attempt to view and import the workflow I get the following error: The owner of this workflow has disabled imports via this link. You can return to the previous page

Re: [galaxy-dev] Issues importing a shared workflow

How did the user share the workflow with you, via link or directly with your user? And which import option are you using? Does "Clone" in the workflow context menu work? -Dannon On Feb 24, 2012, at 3:25 PM, Iry Witham wrote: > I have a Galaxy user who has created a workflow from a history an

[galaxy-dev] different number output files generated based on user parameter

Thank you Shaun. That worked really good! One final question. What is the best way to generate output files dynamically by galaxy. That is if the user sets a parameter, say create bam file. Then the output file gets generated. If the same parameter is false or no, then galaxy does not generate t

[galaxy-dev] cannot startup the local instance of tool shed

Hello everyone, I'm a new to Galaxy and the tool sheds. Right now i am learning it by reading the tutorial and have a problem: when i try to start my local tool shed by typing the command "%sh run_community.sh" within the galaxy installation directory, nothing happens. It just terminate itself im

Re: [galaxy-dev] [Newsletter] Re: Issues importing a shared workflow

He opened the workflow in his history and clicked options, Share or Publish and added my email address. When I attempted the import I click on "View" in the context menu to open the workflow. I then click "Import Workflow" in the upper righthand side of the window. I can clone it just fine. Iry

[galaxy-dev] GATK metadata problems

When I try to run a GATK analysis that uses a bam file as input, I get the following error in the html page: Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue. when the input file is a bam file that has not run yet or is still run

Re: [galaxy-dev] cannot startup the local instance of tool shed

Hello Tyler, When using the public Galaxy tool shed while learning, please use the test instance of the tool shed rather than the production instance. I noticed that you uploaded the filter tool from the Galaxy distribution to the main tool shed. The public test tool shed is available at htt