The Galaxy Web API is documented here: http://wiki.g2.bx.psu.edu/Learn/API
-- jt
On Tue, Oct 9, 2012 at 6:30 AM, harry humphries harry...@gmail.com wrote:
We are trying to develop a plugin for drupal CMS that interacts with the
galaxy api, basically we want to create a control panel for the
Hi Pieter,
We've disabled Bitbucket tickets for now, and we're evaluating better ways to
track issues and enhancements. We'll soon have a public form of issue tracking
again, and issues you've already submitted should be available there. I'm not
sure what the timeline on this is, but we'll
Dear All,
Could you please tell where or how I could get the list of
multi-threaded tools and the amount of threads they open by default?
Thanks a lot
Jean-François
PS: I have collected the following list by hands:
#Tool_idNum_thread
gatk_count_covariates4
Hi List,
Our tools require an array of input files and also produce an array of files.
This seems as a pretty standard task, but unfortunately Galaxy doesn't support
this yet.
I wonder if somebody has already implemented this kind of 'file array' data
type?
I.e. the user selects a local
Hi,
I have a question about param tag. I need to pass the parameter $
__user_email__ part of the galaxy variables reserved for the default value
of a parameter that I am creating
example:
name=email / param value=$__user_email__ ..
Has someone done this before?
Thank you !
--
*Alfredo
Thanks Greg,
Indeed, I tried to be smart and removed the entries from tool conf xml
before running the script. :)
About the missing dependencies, I still couldn't make it happy. I have
added:
$GALAXY_ROOT/tool_dependency_dir/bwa/0.5.9/env.sh
and add appropriate export PATH inside the env.sh,
Hi,
I have an executable tool that input parameter is an xml string
(e.g. run.sh examname/exam), so how should I set the
configfile tag('configfileexamname/exam/configfile' is not right)
if the tool is called by using a tmp-file in command tag (i.e. run.sh
$tmp-file) ?
thanks
welkin
Okay,
I found the button for installing the dependencies. The files are installed:
galaxy-dist/tool_dependency_dir/bwa/0.5.9/devteam/bwa_wrappers/ffa8aaa14f7c
Quite different from what the wiki states..
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Derrick
On Wed, Oct 10, 2012
