Hi Bernado,
can you try to change your $HOME/shed_tools to a full path?
Also please try my small tutorial here:
https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
Hope that will help you!
Cheers - Bjoern
Am 08.04.2014 23:39, schrieb Bernardo Bello:
Hi,
I am having
Philip
Using a the first column as label should work if you tick the box
Include a third column as data point IDs?
Regards, Hans-Rudolf
On 04/09/2014 07:47 AM, Philippe Moncuquet wrote:
Hi Hans-Rudolph,
Ok so the syntax in the wrapper was not the problem. My file was tabular
but the first
Hi Nik
I don't think there is a solution out of the box for all of this, but I
will try to give you some pointers - others might have different or even
better suggestions (my suggestion are very 'hacky'). Let me answer your
questions in reverse order:
- Instead of using Add another file,
Hi,
While problems are been solved in my other Galaxy instance (MAC OSX), I
tried to install Galaxy on local Linux machine running Ubuntu 12.04.
Surprisingly, seems I have been able to get Galaxy toolshed work. The
problem I have now is that I'm trying to run a published workflow, named '
Hi all,
In discussion about adding an NCBI BLAST data manager
https://github.com/peterjc/galaxy_blast/issues/22 based on
Dan's example, Michael Li has suggested using the new(ish)
Data Table functionality of Galaxy for using *.loc files:
https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
Hi all,
I have some doubts about how to configure a LWR server on Linux.
I have read the LWR documentation, however how to configure the LWR is not
clear to me.
This is my scenario:
On my Galaxy server I have some tools that I would like to send their jobs
to the LWR server. These tools are at
Greetings,
I am adding a new tool to our in-house Galaxy, which has a few string inputs. I
have made each one a text param in the XML, but want to ensure that the user
does not leave any empty when he executes the tool.
How can I do this? I tried setting the optional field of each text param
Hi Peter,
Having a standalone repository that just contained the tool data table and .loc
file that could be a dependency of other repositories would be a good way to go
here. Unfortunately, this isn’t supported right now. I’ve opened a trello card
for this: https://trello.com/c/VZxV08Qt
On Wed, Apr 9, 2014 at 4:14 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
Having a standalone repository that just contained the tool data table
and .loc file that could be a dependency of other repositories would
be a good way to go here. Unfortunately, this isn’t supported right
Hi Björn,
I finally got Galaxy tool shed working, installing Galaxy again following
your tutorial and worked. Just skipped the san-boxed optional step.
Thanks,
Bernardo
2014-04-09 9:04 GMT+02:00 Björn Grüning bjoern.gruen...@gmail.com:
Hi Bernado,
can you try to change your
This has been solved. Detrprok workflow is working well, although asRNA
step not. I will contact the author for this particular problem.
Thanks, Bernardo
2014-04-09 11:04 GMT+02:00 Bernardo Bello popn...@gmail.com:
Hi,
While problems are been solved in my other Galaxy instance (MAC OSX), I
Hi Nate,
I just wanted to share my experience about this issue. We sometimes have
a big number of those jobs in limbo (new, waiting or paused). When we
restart Galaxy, I saw that this has an impact on the job handlers. The
job handler seems to be adding the new jobs to the job handler
Hi Nicola,
Thank you. I tried the validator as you illustrated, and it worked
perfectly.
--
Ravi Sanka
ICS Sr. Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
--
On 4/9/14 11:06 AM,
As far as I can figure out, the parameter map for running a workflow via the
API is supposed to look like this:
{'blastn': {'param': 'evalue', 'value': '1e-06’}}
This doesn’t seem to allow for multiple parameters to a single tool. Is there a
way to submit multiple parameters that I’m missing?
The API interface is translating my parameters into python repr strings instead
of actual strings.
A command that should look like this:
createPrimerFile.py
/minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NN NN
I have a set of galaxy generated bam and bigwig files containing over 600
contigs. When I attempt to view any of these files with trackster (on a local
server running current galaxy-dist) I get the following in my log file:
galaxy.webapps.galaxy.api.datasets ERROR 2014-04-09 17:41:16,063 Error
I’ve figured this one out. The tool id changed one me. Sorry for the spam.
-j
On Apr 9, 2014, at 4:48 PM, John Marmaduke Eppley jmepp...@mit.edu wrote:
The API interface is translating my parameters into python repr strings
instead of actual strings.
A command that should look like this:
The API interface is translating my parameters into python repr strings instead
of actual strings.
A command that should look like this:
createPrimerFile.py
/minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NN NN
As far as I can figure out, the parameter map for running a workflow via the
API is supposed to look like this:
{'blastn': {'param': 'evalue', 'value': '1e-06’}}
This doesn’t seem to allow for multiple parameters to a single tool. Is there a
way to submit multiple parameters that I’m missing?
Hi,
Can someone point me in the direction of where the code in Galaxy is called
to change the history background for example when a job changes from Yellow to
red on error, or yellow to green on success. I've been going around in circles
now trying to figure out, how this is implemented
Hi,
how is the Browse... button implemented on the data upload tool page?
When you click on it you get a new window appearing so you can select files to
upload.
Does anyone know where is the Browse... button is defined/implemented in the
code? I thought it would be in
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