Re: [galaxy-dev] Redirecting page after tool completes

Yes. I'm looking to auto display the final history output when the job finishes. It's pretty traightforward to get the URL to display i.e. http://'servername'/capaibl/datasets/5a1cff6882ddb5b2/display/?preview=True. However, I don't know how to use the URL to set it on the galaxy webpage. i.e.

[galaxy-dev] error: flexbar dependency is not installed by the toolshed

Hi Guys, I tried to install flexbar from toolshed, but upon running, error said it could not find it. I checked and found toolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4 in the config file, but this path does not exist. Is it that I need to install the dependency on my own? I had the

[galaxy-dev] The main Tool Shed is now tracking the next-stable branch in preparation for the upcoming Galaxy release

Hello all, The upcoming Galaxy release is currently scheduled for Monday, June 2. In preparation for this release, the main Galaxy Tool Shed is now tracking the next-stable branch and is currently running changeset 13542:11403745e7ce. The main Tool Shed will be regularly updated with any addi

[galaxy-dev] GCC2014 Early Registration closes this Friday, May 23

Hello all, This just a reminder that early registration for the 2014 Galaxy Community Conference (GCC2014) *closes this Friday, May 23* Register early and *avoid paying 70% more for regular regi

Re: [galaxy-dev] Get the user credentials from the tool.

Hello John, Thank you very much for the very extended response. It seems I have enough reading to be calm for a month :-). Thank you again, Dmitry On 5/19/2014 4:42 PM, John Chilton wrote: Hello Dmitry, Sorry the delayed response. It occurs to me that data source tools may be an alternative

Re: [galaxy-dev] Fwd: InvalidVersionError: 103 is not 105

Ok, great, glad you're up and running! I'll scratch this one off the list of things to think about. On Mon, May 19, 2014 at 4:00 PM, Evan Bollig wrote: > Hey Dannon, > > I managed to resolve this on my own. > > The postgres version is 9.1, and I'm on Ubuntu 12.04. The instance is > an OpenStac

Re: [galaxy-dev] Fwd: InvalidVersionError: 103 is not 105

Hey Dannon, I managed to resolve this on my own. The postgres version is 9.1, and I'm on Ubuntu 12.04. The instance is an OpenStack VM. It turned out that the dir contained files that were outdated from a previous version of galaxy-dist. After I realized that they were part of hgignore, I ran "hg

[galaxy-dev] workflow delete cancelled but workflows are still deleted

I am working in the galaxy-dist stable branch. I select a workflow and select "Delete". An alert pops up asking if I'm sure I want to do that. I press "Cancel" and the alert disappears, along with the workflow. This shouldn't happen. Cheers, -Evan Bollig Research Associate | Application Developer

[galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files

Hi Greg, Dave, I just tried to upload an updated tar-ball to the Test ToolShed and got a red error message: Uploaded archives can only include regular directories and files (no symbolic links, devices, etc). Offender: Note no offending files were listed. When I double checked I had prepared my

Re: [galaxy-dev] user specific access/options

Hi Emma Have a look at https://wiki.galaxyproject.org/Admin/Config/Access%20Control and https://wiki.galaxyproject.org/UserDefinedToolboxFilters as an alternative you could also do a bad hack using "dynamic_options" Regards, Hans-Rudolf On 05/19/2014 10:38 AM, Emma Prudent wrote: Hi, I

Re: [galaxy-dev] Get the user credentials from the tool.

Hello Dmitry, Sorry the delayed response. It occurs to me that data source tools may be an alternative I should have pointed you to right away - https://wiki.galaxyproject.org/Admin/Internals/DataSources. I am not sure they are a perfect fit but regular tools are not a perfect fit either. On Tue,

Re: [galaxy-dev] user specific access/options

Hi, I am currently an intern and I work on galaxy, particularly on this acces problem. So I am very interested in the answers that could be given to this question. Thanks to you, Emma Prudent Hi Petr, I am going to forward your email to the galaxy-dev list so that the development community

[galaxy-dev] InvalidVersionError: 103 is not 105

I have an empty posgresql database: psql -c "create database galaxy;" I'm trying to launch run.sh from the latest version of galaxy-dist. Migration proceeds normally up to this point: # galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:

Re: [galaxy-dev] replacing XML fragments in mycustomtool.xml

On Mon, May 19, 2014 at 9:29 AM, Pierre Lindenbaum wrote: > This question was cross-posted on https://biostar.usegalaxy.org/p/7619/ > "Adding custom tools: resolving (external ) XML entities" > > I'd like to replace fragments of XML code in my custom tool declaration. > > My first idea was to use

Re: [galaxy-dev] monitoring jobs start time

Il 2014-05-19 04:47 neil.burd...@csiro.au ha scritto: Hi, I am currently using the reports tool to see what jobs have been executed etc ... When you look at the information for each job it states the time the job was put on the queue (creation time) not the actual start time of the job. Do you

[galaxy-dev] replacing XML fragments in mycustomtool.xml

This question was cross-posted on https://biostar.usegalaxy.org/p/7619/ "Adding custom tools: resolving (external ) XML entities" I'd like to replace fragments of XML code in my custom tool declaration. My first idea was to use XML entities but it seems that the XML engine doesn't resolve them

Re: [galaxy-dev] Redirecting page after tool completes

Not that I am aware of, but given the run time of jobs is quite variable it seems confusing to have Galaxy suddenly switch focus - especially if I have another tool or visualisation open, or am looking at a particular datafile. However, if the user hasn't interacted with Galaxy since pressing the