[galaxy-dev] RNA-seq

2014-01-29 Thread Karla Fernández Cano
Hi, My name is Karla Fernández a student of a University in Nuevo Leon in Monterrey, Mexico (UANL). The reason for this mail is because i'm going to work with differential gene expression of the yeast Pichia pastoris and i'd seen that the complete genome and annotations of this yeast are absent in

Re: [galaxy-dev] datatype for executables

2014-01-29 Thread Ketan Maheshwari
Thanks for your answer. Yes, the idea is to have runnable executables such as executable binaries and shell scripts to run via a parallelizing tool Swift. As for security, current plan is to run Swift enabled Galaxy tools in controlled cloud instances, which we are already doing. With this datatyp

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-01-29 Thread Greg Von Kuster
Hi Peter, On Jan 29, 2014, at 12:55 PM, Peter Cock wrote: > Hi all, > > Are both the main and test Tool Sheds currently meant to be running > nightly tests again? > Yes > I've not really got back into Galaxy tool testing since Christmas. > Most of my tools' > test results look sensible, but

[galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-01-29 Thread Peter Cock
Hi all, Are both the main and test Tool Sheds currently meant to be running nightly tests again? I've not really got back into Galaxy tool testing since Christmas. Most of my tools' test results look sensible, but there seem to be some issues still, e.g. http://testtoolshed.g2.bx.psu.edu/view/pe

Re: [galaxy-dev] Error when searching for tools in local instance.

2014-01-29 Thread Perez, Ricardo
Hi Sam, No it did not fix the issue. When I checked we were in fact in the stable branch. I am sorry for my delayed response, --Ricardo Perez - Original Message - From: "sam guerler" To: "Ricardo Perez" Cc: "Galaxy-dev Galaxy-dev" Sent: Friday, January 24, 2014 5:21:56 PM Subject: R

Re: [galaxy-dev] sysadmin help

2014-01-29 Thread Nate Coraor
Hi Donny, Thanks for the heads up about the broken link, I've fixed it. Other than that, are you running in to problems connecting Galaxy to your existing cluster? --nate On Tue, Jan 28, 2014 at 9:29 PM, Shrum, Donald C wrote: > Hi all, > > I could use a little basic help. I'm setting up a pr

[galaxy-dev] Problem with editing permissions on Galaxy libraries

2014-01-29 Thread Christophe Antoniewski
Hi, Since an undetermined period of time in our instance, the "edit permission" panel under admin management of libraries shows an unexpected aspect: The "modify library item" part of the form is normal, with 2 fields for Roles associated and Roles not associated. However, none of the other parts