On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:
Hi Rudolph,
Thanks for the answer. I understand that it would make no sense to allow
generation of graphics on non relevant data. My data is in tabular
format and that is the reason why I was surprise not to see that button.
outputs
Hi Brad,
thanks for your patch. Do you mind to create a pull-request to my github
account?
https://github.com/bgruening/galaxytools
Otherwise, are you ok if I push it and reference you by name?
Also, it would be good the make the non-sorting optional. Many of us
using the calling program
Better test it to make sure ;)
Of course, if you really want the use the *.loc file as a static configuration
file which should be updated in sync with the tool code, that might be a
problem...
Peter
On Mon, Apr 7, 2014 at 11:09 PM, Dooley, Damion damion.doo...@bccdc.ca wrote:
Oh, great! I'd
Thanks. Finally it worked!! I pass the solution:
My python file:
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o +sys.argv[2]
os.system(cmd)
Ok,
a small update on this problem.
I have set up a local tool shed with in it a repository that holds 2
tool definitions of the same tool but with different verision nbrs
tool id=NicybDummyTool name=Nicyb Dummy Tool version=1.0
descriptionDummy Tool/description
command interpreter=python
Hi Adhemar,
Very glad this is working out for your own use. I created a ticket to
include your suggested enhancement globally:
https://trello.com/c/jbhy3dSM
Should you wish to create a ticket in the future, this is how:
https://wiki.galaxyproject.org/Issues
Community contributions are
Hey Brad, thanks for this! I've added these to the metaphlan toolshed
repository as-is, and will be adding tests shortly.
On Tue, Apr 8, 2014 at 1:24 AM, Langhorst, Brad langho...@neb.com wrote:
I'm running with these local additions to Dannon's metaphlan repo.
I think it would be better
Hi there all,
Does anyone have RPY working? I install via toolshed and the folder is empty,
and shows missing dependencies.
I have searched previous posts, nothing since 2010. I have a local install
(production config - postgres, etc - on CENTOS 6.5). I posted last week and it
fell off the
Hello Curt,
I believe that version 1.0.3 of the rpy package should be installing
successfully from the main tool shed if you have a repository that contains a
tool that defines a dependency to the rpy repository owned by devteam at
http://toolshed.g2.bx.psu.edu/view/devteam/package_rpy_1_0_3
Hi,
I am having problems to install a tool from tool shed named S_MART on my
local Galaxy. In fact, its the first tool I'm trying to install.
The reason to install S-MART is to use DETR'PROK in Galaxy.
Here is the 'error' Galaxy shows after installing some programs from
There is no mechanism in Galaxy for doing this. Galaxy for the most
part (or entirely?) does not use extensions for determining data
formats - datatypes define sniffer methods and the sniffing methods
all inspect the data on the filesystem so require completed uploads
and in turn the upload
Hi all,
We have a local install of Galaxy that we use for testing for our
bioinformatics courses. I am creating some new tool interfaces for the
install. I want to create a tool that will allow a user to automatically
add a fasta database to the built-in databases (without needing to reboot
the
Hi Hans-Rudolph,
Ok so the syntax in the wrapper was not the problem. My file was tabular
but the first column contained string and numbers whereas the second column
contained only numbers. When I added a 3rd column with numbers to test I
was able to see the button and generate some graphics. I
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