Hi Greg,
I just changed the public name on the web interface, where you click on the
User dropdown, and choose Public Name. Something about my environment let it
happen, when it apparently should have not been possible.
I suspect the reason lies in some mismatch between my apache user
authent
I do not know what happened but I keep getting the following issue when I try
to start my Local Galaxy. Can someone tell me how to fix this issue please?
Starting galaxy...
Traceback (most recent call last):
File "./scripts/check_eggs.py", line 32, in
from galaxy.eggs import Crate
ImportE
Hi Björn,
> There is a version in the testtoolshed, I can migrate it if you like and
> if you can confirm that you can install it :)
I'd be very interested in the infernal wrapper! I'll try to install it.
> The problem is that you do not have defined your tools in the
> tool_dependencies.xml fi
Hello,
The easiest way to ensure that dependencies are set up correctly is to
install tool dependencies directly from the Tool Shed:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency
You will want to use:
http://toolshed.g2.bx.psu.edu
Hi Wolfgang,
I am going to re-post your question over to the galaxy-dev mailing list,
which is best for local instance questions. To all: please remove the
galaxy-user list from any replies.
Thanks!
Jen
Galaxy team
On 9/5/13 1:33 AM, Wolfgang Maier wrote:
Hi everybody,
I'm trying to add the ve
Hi,
I started getting the following error whenever I try to load a file into Galaxy
local.
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in
from galaxy import eggs
ImportError: cannot import name eggs
I will appreciate if so
Hi Joahcim,
Thanks so much for your reply. The problem has actually been resolved
thanks to a response from Federico Zambelli. Embarrassingly, it did not
occur to me that because the passwords had been created while PBKDF2
encryption was enabled, that I would need to reset them after disabling
it
now i got it,,
On Thu, Sep 5, 2013 at 5:34 PM, Dannon Baker wrote:
> That's weird, the board is public. Are you able to go to the root
> development board? https://trello.com/b/75c1kASa
>
>
> On Thu, Sep 5, 2013 at 11:32 AM, Zeeshan Ali Shah wrote:
>
>> Dannon, i could not get access to that
I have migrated few tools from dist to tool-shed and I am seeing two version
select options in the UI. Both option contain same version number though. One
of them is linking to dist path (underneath tools directory) and other one is
using tool-shed path. The dist path isn't in place after the m
Hi,
This is Deblina. I am working as a PhD student in Martin Luther
University Wittenberg, Halle, Germany. For a project I want to use
Galaxy. I need to construct a master workflow with sub-workflows
connected to each other.
Is it possible to construct "workflows of workflows" in galaxy?
Hello Simon,
The tool shed middleware basically consists of 2 files in
~/lib/galaxy/webapps/tool_shed/framework/middleware: hg.py which handles
authentication when pushing from the command line. The remoteuser.py file
handles remote user authentication, but I cannot guarantee it properly handl
That's weird, the board is public. Are you able to go to the root
development board? https://trello.com/b/75c1kASa
On Thu, Sep 5, 2013 at 11:32 AM, Zeeshan Ali Shah wrote:
> Dannon, i could not get access to that trello page. can you kindly invite
> me ? zas...@pdc.kth.se
>
>
> On Thu, Sep 5,
Dannon, i could not get access to that trello page. can you kindly invite
me ? zas...@pdc.kth.se
On Thu, Sep 5, 2013 at 5:31 PM, Dannon Baker wrote:
> The iRods integration is under active development, follow progress here:
> https://trello.com/c/Sp9XvRfD/1072-object-store-write-an-irods-plugin
The iRods integration is under active development, follow progress here:
https://trello.com/c/Sp9XvRfD/1072-object-store-write-an-irods-plugin.
-Dannon
On Thu, Sep 5, 2013 at 11:27 AM, Zeeshan Ali Shah wrote:
> Hi All, Is there any update on iRods integration in galaxy ? One major
> concern pr
Hi All, Is there any update on iRods integration in galaxy ? One major
concern presented in deployment of Galaxy is that all of the researcher
data is access by a user id (linux) running galaxy server. This is typical
webserver problem.
May be it is some how resolved by iRods or any other better
Hi Lionel,
> Bjoern and others,
>
> I'm back at that. I published my tool on the toolshed
> (http://toolshed.g2.bx.psu.edu/view/lionelguy/prokka). I created a new,
> fresh instance of galaxy from scratch, with a new database. I went on
> and installed prokka from the toolshed. Prokka has a lot
Bjoern and others,
I'm back at that. I published my tool on the toolshed
(http://toolshed.g2.bx.psu.edu/view/lionelguy/prokka). I created a new,
fresh instance of galaxy from scratch, with a new database. I went on
and installed prokka from the toolshed. Prokka has a lot of
dependencies, that
I suspect there is an issue with Trackster when changing from one mode to
another. Can you confirm that by saving and refreshing the visualization, you
can view the dataset in different modes?
Thanks,
J.
On Sep 5, 2013, at 4:06 AM, Joachim Jacob | VIB | wrote:
> Update: the 'dense' option does
Hello Simon,
On Sep 4, 2013, at 5:13 PM, "Guest, Simon" wrote:
> Hi Dave, Greg,
>
> Thanks for your reply.
>
> I'm running a recently checked out stable branch. hg log shows this tip:
> changeset: 10473:c42567f43aa7
> tag: tip
> user:greg
> date:Mon Aug 19 13:19:5
Hi Björn,
Thanks for your help!
This was just a development version, the tool is on the toolshed (prokka). I
wanted to test the dependencies before releasing the toolshed version, but I'll
go and release, and test from there.
Cheers,
Lionel
On 5 Sep 2013, at 13:21 , Bjoern Gruening wrote:
>
Hi Lionel,
>
> I've been scratching a bit my head about how galaxy builds dependency,
> fruitlessly so far... Here is my problem: I have a local tool (not
> installed through a toolshed) that makes use of another tool (aragorn)
> that I installed from the toolshed.
>
> Aragorn requires the ar
Hi Galaxians,
I've been scratching a bit my head about how galaxy builds dependency,
fruitlessly so far... Here is my problem: I have a local tool (not
installed through a toolshed) that makes use of another tool (aragorn)
that I installed from the toolshed.
Aragorn requires the aragorn pack
Hello Adam,
maybe this is a stupid question, but do you have reset the password for
the user you are attempting to login via proftd after you disabled
PBKDF2 in universe_wsgi.ini? If not, the password is still encoded with
PBKDF2 in the db and thus it will never work with SHA1 authentication.
Hi Adam,
I remembered having a hard time getting this to work. After it worked,
networkadmins decided to disallow ftp connections at our university due
to security concerns...
I do not remember the solution (...), but I can share my config files (I
am using apache instead of nginx):
This
Update: the 'dense' option does not work neither. So in summary: the
alignment can only be viewed in 'coverage' mode.
Thanks,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/05/2013 09:52 AM, Joachim Jacob | VIB | wrote:
Hi all,
I have a problem
Hi all,
I have a problem that the mappings of an experiment suddenly don't show
up anymore in Trackster, only when I choose 'squish' as visualisation
format. 'Coverage' and 'dense' provide the expected output. So 'squish'
shows nothing. But 'Pack' shows only the names, without the bars. Note:
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