Hi,
I stopped toolshed, dropped the database, and recreated it.
Relaunched toolshed without errors. I have create a login again, created
a category (no problems), and tried to create a repo, which upon saving
gives me the error again.
Is it a problem that I use the same user for access to
On Tue, Apr 3, 2012 at 1:57 AM, Xu, Jianpeng jianpeng...@emory.edu wrote:
Hi,
I have installed our local galaxy. I have a question for Fastq Groomer:
Is it an interior tool within Galaxy ? I mean you already incorporate it
into Galaxy? Or, you incorporate an external tool into Galaxy ? Do
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to make this kind of documentation
more visible...
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to
Hi Greg,
I'm afraid to say I might have been a bit ahead of myself in asking you to
create that Proteomics category. We're almost ready to upload our tools, but
at the last minute we've discovered a bunch of issues we need to sort out.
I'm going away for Easter and won't be back until the
No worries, Ira - have a great Easter vacation!
On Apr 3, 2012, at 7:20 AM, Ira Cooke wrote:
Hi Greg,
I'm afraid to say I might have been a bit ahead of myself in asking you to
create that Proteomics category. We're almost ready to upload our tools, but
at the last minute we've
Hi,
I have installed the local galaxy. I am trying to run some programs.
I have a question now:
If I run a program and the output file will be in the history. If I want to do
something with the output file, it looks like I have to download it at first.
Is there a way to do something with the
Every time I run Picard's AddOrReplaceReadGroups, my system tmp directory
fills, and the tool stops. I'm left scratching my head, because it seems
that the JVM sets the system /tmp directory on my local galaxy-central
branch, instead of the new_file_path I have defined in universe_wsgi.ini.
This
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Invalid tools are now displayed in the Preview tools and inspect metadata
by tool version section - here is the list for the hmmer repository.
Lovely - that will help with the existing tools which are not all
fully
Hi, Matt.
Thanks for reporting this - it's definitely a misfeature...
The tool wrapper tools/picard/picard_AddOrReplaceReadGroups.xml does
not explicitly set the tmpdir parameter, so I've added --tmpdir
${__new_file_path__} to the command line generated. That will
over-ride the default value /tmp
On Mar 9, 2012, at 4:12 AM, Yuri D'Elia wrote:
Hi everyone. I've set up a galaxy production environment and it seems to be
working.
I've identified a couple of issues though:
If I enable apache_xsendfile, the little eye icon (Display data in
browser) on each dataset stops working. I get
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