Hello Galaxy People!
(it's been a while since I've last been here... a pleasure to be back).
I intend to publish a small command-line utility, which will also be available
through Galaxy Toolshed.
It'll be a small application note, so not a lot of space for many citations.
The relevant
Dear John and the Galaxy team,
Thank you for your prompt response however, I am still getting the same error
that I reported previously. I attempted to load the data again at 9:45am
Central Time on Wednesday March 26th, and received the following error
Errors were encountered loading the
Hi Guys,
is it possible to add E.coli K12 genome for mapping with Bowtie on
Andromeda-NCBI portal?
thanks,
timur
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Hi Jeremy,
I cleaned the catche on both safari and firefox, but it doesn't work. It still
shows the same error messages.
Thank you very much for the help!!
Best,
Shu-Yi
On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote:
This sounds like a cache issue. Both of these scripts have been removed
I'm using galxy-dist. That's why I don't have the setting. Thanks for
the information, I'll wait for the next stable release and update the
settings then.
Geert
On 03/26/2014 01:59 PM, Greg Von Kuster wrote:
The changeset that made this a configurable setting was committed to
the stable
Hi,
I have implemented a custom tool which will parse a given string in to
expected format. Installed this custom tool into galaxy and was able to run
successfully.
I would like to add test cases to this tool, can you please provide me
resources to write test cases for this custom tool.
Is this
Hi,
I found below resources:
- Running
testhttps://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests
- Writing Functional
testshttps://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests
Thanks,
JanakiRam
On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama
Hi, I tried to GROOMER my fastq data in fastq data, and galaxy did not allowed
me:Error executing tool: objectstore, __call_method failed: get_filename on ,
kwargs: {}could you please help me?Thank you
viR
Hi,
I have added tests to tool dependency xml, but how should I run these
tests, can you please help me to run test cases.
.
tests
test
param name=input1 value=some string/
param name=input2 value=expected format/
output name=output
As Janaki replied below, see:
http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests
On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:
Hi,
I have added tests to tool dependency xml, but how should I
Hi,
Thanks for reply. I composed a details email for better clarity.
when run grep command in galaxy home folder ( ./run_functional_tests.sh
-list | grep barcode-parse), I got no results.
What I did was:
- Implemented a custom tool (It has one python script and tool
definition file. These
Hello Janaki,
Thanks for clarifying that you have installed your tools from a Tool Shed. In
this case, functional tests do not use Galaxy's tool_conf.xml.sample, so
changing it will make no difference. For information about running functional
tests on tools installed from the Tool Shed, see:
Thank you, I will go through the resources and will reply my results to
this email chain.
Thanks,
JanakiRam
On Thu, Mar 27, 2014 at 6:39 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Janaki,
Thanks for clarifying that you have installed your tools from a Tool Shed.
In this case,
Hi,
I added your request to the card where we track these:
https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card
Martin
Galaxy team
On Wed, Mar 26, 2014 at 3:17 PM, t...@caltech.edu wrote:
Hi Guys,
is it possible to add E.coli K12 genome for mapping with
Hey Assaf,
For Cite1 (Galaxy): doi:10.1186/gb-2010-11-8-r86
For Cite2 (ToolShed): doi:10.1186/gb4161
Thanks for asking!
-- jt
On Tue, Mar 25, 2014 at 1:15 PM, Assaf Gordon agor...@wi.mit.edu wrote:
Hello Galaxy People!
(it's been a while since I've last been here... a pleasure to be
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