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 worki
On Feb 23, 2012, at 5:13 PM, Derrick LIN wrote:
> Hi guys,
>
> I have setup a test galaxy and configured Apache as proxy. It's been running
> fine when I did all testing on my machine with Chrome.
>
> Recently, I let some of my colleagues to try it out, then they experience
> some file downloa
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 "/tm
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster 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 compliant with th
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
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 o
On Mar 19, 2012, at 9:34 AM, Peter Cock wrote:
> On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster wrote:
>> With regard to tool validity, the definition of a valid
>> tool in the tool shed has always been restricted to the tool properly
>> loading in a Galaxy instance. If a tool is not valid,
Hi Greg,
- Toolshed uses a separate (from Galaxy) postgres database, called
toolsheddb.
- Mercurial has version 1.4. <--- THIS IS THE PROBLEM (default in the
repo of Centos6.2) -- see below
[quote] The hgweb.config file should be automatically created in your
Galaxy install directory when yo
On Apr 2, 2012, at 11:03 AM, Ann Black-Ziegelbein wrote:
> Hi all -
>
> In running a samtools sort, we experienced the following exception from
> Galaxy:
>
> galaxy.jobs.runners.drmaa ERROR 2012-04-01 12:01:27,200 Job wrapper finish
> method failed
> Traceback (most recent call last):
> File
On Apr 2, 2012, at 1:43 PM, Robert Chase wrote:
> Hello,
>
> I am trying to fix something that I see in my paster.log file. At the end of
> the file, after everything has been loaded and the server is running, I get
> an error message saying that bz2 cannot be imported. When I start a python
Hello,
I am trying to fix something that I see in my paster.log file. At the end
of the file, after everything has been loaded and the server is running, I
get an error message saying that bz2 cannot be imported. When I start a
python interpreter session and type in "import bz2" it runs without
in
Hello,
I configured our local galaxy to allow data displaying in the GBrowse
I got this error when I was trying to display some data from our
galaxy at wormbase GBrowse.
-
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 dis
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 1
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster 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 t
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster 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...
>
> I
On Tue, Apr 3, 2012 at 1:57 AM, Xu, Jianpeng 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 you know
> some p
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 bo
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