Hi Jordi
Have you looked into using "Data Libraries", see:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Your anonymous users can then select any of the prepared data sets (via
the 'Shared Data' tab), a
Hi Saliya,
the Galaxy documentation is a good starting point for your questions:
http://wiki.galaxyproject.org/
http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
Also have a look at the Tool Shed:
http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
You can search for G
Hi james,
49: 1.bigwig
20.7 KB
format: bigwig, database: ?
uploaded bigwig file
display in IGB Local Web
I have uploaded 1.bigwig file in this https://main.g2.bx.psu.edu/ galaxy .
but when i clicked Web option . it creates a ".jnlp" file . I am not able to
see anything on web . how t
Hi james,
can you share some examples of display application . and in which tool you use
for display application in galaxy ?
Regards
shashi
From: James Taylor
To: shashi shekhar
Cc: Ross ; "galaxy-dev@lists.bx.psu.edu"
Sent: Wednesday, 19 June 2013 7:0
Hi,
I am new to development with Galaxy and wonder if someone could kindly help
me out with the following.
1.) A step-by-step guide on how to develop a tool
2.) Are tools limited to simple functions that run on a single node?
3.) When Galaxy is run on cloud (with EC2) how does it utilize worker
n
Hello Joachim,
What version of Galaxy are you running?
It looks like the 500 error should be displayed in your tool shed's paster log.
Thanks,
Greg Von Kuster
On Jun 19, 2013, at 2:46 AM, Joachim Jacob | VIB | wrote:
> Hi Greg,
>
> Thanks, and sorry for the long delay in response.
>
> To
Hello Joachim and Björn,
This issue should be resolved in change set 10103:d842d50a6ed3, which is
currently running on the test tool shed.
Thanks fro reporting this!
Greg Von Kuster
On Jun 19, 2013, at 6:16 AM, Björn Grüning
wrote:
> Hi Joachim,
>
> confirmed, it seems like a bug.
>
> Ch
Hello everyone,
I am managing an instance of galaxy. We want to provide a set of example
datasets for being used, we want this is by default datasets accessible for the
anonymous user. there is any way to do that?
I have tried to work
the shared and publish option of history but they don't wo
Hi, what roles are embedded in nglims? (am I calling it by the right name?)
I have a "sequencing" role which will be given to anyone submitting a
request, and that seems to be working just fine. I am also using the yaml
form to edit the submission form, and I think it's beautifully implemented.
Hi all,
Again a question from my side in connection with setting up a new Galaxy
instance within an closed network (including a proxy) an SLES 11 SP2.
After some struggeling with the Apache config finally Galaxy was
accessible, but behaves somewhat strange compared to another instance
which is
Tightly integrated interactive visualizations like Trackster need to be web
based (implemented in Javascript). See our paper that just came out in BMC
genomics. Note there is already a phylogenetic tree visualization tool
(phyloviz) that was built by Tomithy Too. Extensions to that for additiona
Hi all,
I am trying to format the input to a java tool that I am writing. I want
to display different options to choose from based on the user input. I am
not sure how to do that.
For example, based on the input file, I want to display the chromosome
options to choose from. How do I do this?
Hi Ross
i got the file registry.py in lib/galaxy/visualization directory .. here four
built in visualization is mentioned ..in the same way i want to add one more
VISUALIZATION in galaxy ...this is my question . i wanted tom know that from
which files i should start .
class VisualizationsReg
Shashi,
Beats me. Cloning the visualisation code would be a good start I'd
guess. It will not be trivial.
Others may have better ideas.
On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar wrote:
> Hi Ross,
> Actually i have to add the visualization which will be interactive . it
> will take datase
Hi Ross,
Actually i have to add the visualization which will be interactive . it will
take dataset from galaxy .it will be in the same way as tracker works .
in stead of tracker i want to add my own visualization tool. from wehere should
i start to replace tracker with my own visulization to
Shashi,
Thanks for the additional information.
AFAIK: If it's command line driven and spews out pdf's, adapt any similar
tool that spews out pdfs like fastqc.
Galaxy tool execution is isolated from the user and from Galaxy itself, so
communication is just not possible if it's interactive - unless y
Hi Ross,
thanks for the reply . actually i want to use TreeView as visulaization tool.
TreeView X is an open source and multi-platform program to display phylogenetic
trees. It can read and display NEXUS and Newick format tree files (such as
those output by PAUP*, ClustalX, TREE-PUZZLE, and oth
Hi Joachim,
confirmed, it seems like a bug.
Cheers,
Björn
> Hi all,
>
> Before posting on Trello, perhaps someone can confirm that it is a bug:
>
> 1. In the admin menu, go to 'Manage installed tool shed repositories'
> 2. click on a tool that you have installed with dependencies (!)
> 3. In
Dear Dannon,
Thanks for your suggestion!
We did give it a try with the backup copy of 10 days back and that worked!
We keep the postgres log and the failed postgres backup (using pg_dump with
both custom and plain text format) for now and will look into what exactly
happened during those 10 days.
Shashi,
Hans made a brave guess based on your vague question, but you'll probably
get better answers if you do us all a favour and make an effort to provide
unambiguous detail about exactly what you want to achieve.
If there is a working Galaxy tool that does what you need but using a
different "vi
Hi all,
Before posting on Trello, perhaps someone can confirm that it is a bug:
1. In the admin menu, go to 'Manage installed tool shed repositories'
2. click on a tool that you have installed with dependencies (!)
3. In the top right 'repository actions', choose 'Manage tool dependencies'
4. In
Hi,
I want to add the the complete separate tool in galaxy . how will i do it ..i
don't want to use existing visulaization tool.
Regards
shashi
From: Hans-Rudolf Hotz
To: shashi shekhar
Cc: "galaxy-dev@lists.bx.psu.edu"
Sent: Wednesday, 19 June 2013 12:
Hi Shashi
Have a look at:
http://wiki.galaxyproject.org/Learn/Visualization
http://wiki.galaxyproject.org/Visualization%20Setup
Regards, Hans-Rudolf
On 06/19/2013 08:07 AM, shashi shekhar wrote:
Hi,
i want to add new visualization tool in galaxy . can i get the required
documents ?
can
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