On Thu, Jan 15, 2015 at 6:57 PM, Ryan G wrote:
> Because of the way the infrastructure for my Galaxy instance is set up, I
> need to download and install tools from the toolshed manually. For most of
> the tools, this is pretty easy, however I'm now trying to add RSEM to my
> instance and it has
Hi Damion,
This change here
https://bitbucket.org/galaxy/galaxy-central/pull-request/639/fix-for-librarydatasettoolparameter/diff
might fix it.
Thanks for reporting the issue,
Sam
On Thu, Jan 15, 2015 at 3:42 PM, Aysam Guerler
wrote:
> Hi Damion,
>
> I will look into this.
>
> Thanks,
> Sam
>
Hi Damion,
I will look into this.
Thanks,
Sam
On Thu, Jan 15, 2015 at 3:30 PM, Dooley, Damion
wrote:
> Hi,
>
> Almost!
>
> def get_initial_value( self, trans, context, history=None ):
>
> in /lib/galaxy/tools/parameters/basic.py under class
> LibraryDatasetToolParameter( ToolParameter ) ge
Hi,
Almost!
def get_initial_value( self, trans, context, history=None ):
in /lib/galaxy/tools/parameters/basic.py under class
LibraryDatasetToolParameter( ToolParameter ) gets past the error. Now a popup
with "Grid failed" appears, with an OK button that cleanly exits (see
attached). S
Eric,
Thanks for the response. That made me take a closer look at the
apache/shibboleth configuration, and it turns out that adjusting some settings
in the shibboleth config fixed the problem.
Mike Waldron
From: Eric Rasche [rasche.e...@yandex.ru]
Sent
Because of the way the infrastructure for my Galaxy instance is set up, I
need to download and install tools from the toolshed manually. For most of
the tools, this is pretty easy, however I'm now trying to add RSEM to my
instance and it has some new datatypes.
Along with the new data types is py
Hi Alexandre,
the commit seems to be also in galaxy-dist now. Anyway,
this command should do the trick:
hg pull -b stable
https://bitbucket.org/galaxy/galaxy-central
I'd suggest you to use
directly the stable branch of galaxy-central, which usually gets the
hotfixes much faster than galaxy-dist
Hi Daniel,
Thanks for the answer.
How can I update my Galaxy instance with this fix? The fix is on
galaxy-central repository and I've cloned the galaxy-dist repository.
Thanks a lot,
Alexandre
2015-01-14 18:29 GMT-02:00 Daniel Blankenberg :
> Hi Alexandre,
>
> Thanks for reporting this issue.
Sorry for the delayed response - I am not really an expert on Galaxy's
egg stuff - but I believe running `python scripts/fetch_eggs.py`
before starting Galaxy usually fixes these problems for reasons I
don't understand. One probably shouldn't need to manually install mock
or pycrypto though.
Sorry
Hi all
For what it's worth, I manually installed mock (and pycrypto because
that was the next thing it complained about) and it worked after that.
Ulf
On 14/01/15 14:23, Ulf Schaefer wrote:
> Hi all
>
> After the announcements this morning, I upgraded to the latest stable
> release as suggested
I thought the difference may be in the -central config handling that didn’t
work with my universe_wsgi anymore or something. Will be hard to trace so I
will leave this for now.
I'll mail you more about the collections though, probably tomorrow.
cheers,
—
Jorrit Boekel
Proteomics systems develop
On Fri, Jan 9, 2015 at 10:42 AM, Jorrit Boekel
wrote:
> Hi all,
>
> I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out
> dataset collections. First thing I run into is that things don’t seem to run
> well when running it on a VM (port forwarded) with nginx. If I click on t
We have an older galaxy installation (uses universe_wsgi.ini config file),
that's configured for external user authentication, provided by our Apache
proxy setup which uses Shibboleth to our campus authentication system. This
works just fine.
I'm setting up a new galaxy installation, the config
Thanks Hans-Rudolf, will do
On 15 January 2015 at 08:24, Hans-Rudolf Hotz wrote:
> Hi Anna
>
> I am just guessing, but it might be worth checking the proxy settings of
> your local galaxy server.
>
>
> Regards, Hans-Rudolf
>
>
>
> On 01/13/2015 05:39 PM, Anna Terry wrote:
>
>> Hi,
>>
>> I am hav
Dear All,
Could someone let me know if there is already a data manager tool for getting
liftOver reference data within Galaxy or should I write one? Please let me know.
Kind regards,
Anne.
--
Dr Anne Pajon - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinso
It was only ever used for one tool that I know of, but we should make
it work since we try to never break backward compatibility. If you add
the 'history=None' kwarg is that sufficient to fix the problem?
However, I think a better solution to this problem is to build it into
dataset parameters. An
Hi Anna
I am just guessing, but it might be worth checking the proxy settings of
your local galaxy server.
Regards, Hans-Rudolf
On 01/13/2015 05:39 PM, Anna Terry wrote:
Hi,
I am having lots of problems with the get data tools installed on our
local galaxy server, I'll start with just one
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