Re: [galaxy-dev] code example for improved error handling

Please see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax . There is a section for ", , and tag sets". The documentation applies to the latest galaxy-dist, though most of what's mentioned (aside from updating stdout and stderr with warning messages) is supported in galaxy-centra

[galaxy-dev] Galaxy Reports no longer functions

Hi Team, Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_weba

[galaxy-dev] TopHat Wrapper to handle Multiple Fastq reads

Greetings, I was working on the TopHat wrapper (we have customized one for handling just one input Fastq read) for handling multiple reads. I figured out that using repeat tag was the way forward, but have been having a hard time with the Cheetah template. Any help or suggestions? Sincerely, Vij

Re: [galaxy-dev] code example for improved error handling

Thanks, greatly appreciated! Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcr...@completegenomics.com From: Scott McManus mailto:scottmcma...@gatech.edu>> Date: Friday, Augu

Re: [galaxy-dev] code example for improved error handling

I'm writing documentation now - I'll have something this afternoon. Sorry for the delay. -Scott - Original Message - > No, I call the executable directly from the xml. It kept failing > although it seemed to finish the job and I realized that on success > the executable prints a summa

[galaxy-dev] grouping/separating parameters on the page

Hello, Is there a way to do one or both of the following: 1) Group a set of related parameters together on a tool page 2) Put a separator in between related groups. I have a tool with lots of parameters. It's ok to have them all on one page but I'd like to have some space or a line between the re

Re: [galaxy-dev] optional="false" not working?

On Fri, Aug 17, 2012 at 12:39 AM, Peter Cock wrote: > On Fri, Aug 17, 2012 at 12:18 AM, Dan Tenenbaum wrote: >> Hello, I have the following wrapper: >> >> >> foo >> >> tool.py $outputFileName >> >> >> > optional="false"/> >> >> >> >> >> >> >> I expect that

[galaxy-dev] Track jobs in database should be True? Re: Shell script to start Galaxy in multi-server environment

On 8/16/12 4:18 PM, "Karger, Amir" wrote: >On 8/8/12 4:06 PM, "Nate Coraor" wrote: >> >>If you aren't setting job_manager and job_handlers in your config, each >>server will consider itself the manager and handler. If not configured >>to run jobs, this may result in jobs failing to run. I'd su

[galaxy-dev] cuffdiff output

Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff t

Re: [galaxy-dev] optional="false" not working?

On Fri, Aug 17, 2012 at 12:18 AM, Dan Tenenbaum wrote: > Hello, I have the following wrapper: > > > foo > > tool.py $outputFileName > > >optional="false"/> > > > > > > > I expect that when I click "Execute" I will be told that "tp" must > have a value. Ho

Re: [galaxy-dev] FTP upload - symlink to uploaded data

Hi Nate, thanks. Do you know what's the reason for using copying first the contents to the /tmp directory, before copying it into a the database/files/... Seems inefficient to do so, or is this not how it works perhaps? Regards, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaa

Re: [galaxy-dev] Problem installing local instance of Galaxy

Hi Kenneth If you try to connect to "localhost" using your PC, it will search for a (galaxy)server on your PC. Hence, you need to replace with the name or IP adress of the server where Galaxy is running Regards, Hans On 08/17/2012 03:24 AM, Kenneth Watanabe wrote: To Galaxy, I installed Ga