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 at
Hi,
I have an executable tool that input parameter is an xml string
(e.g. run.sh name), so how should I set the
configfile tag('name' is not right)
if the tool is called by using a tmp-file in command tag (i.e. run.sh
$tmp-file) ?
thanks
welkin
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, re
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" /> ___
Please keep all replies on the lis
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 dire
Hi Joel,
I can provide a couple of comments, or better yet start a discussion, but
others please feel free to chime in.
> 1) How will this work with the concept of a tool volume snapshot? I'd have
> to make a snapshot of my partition every time I installed/removed a tool
> from a tool shed. Would
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
gatk_realigner_target_creat
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 co
Bjorn,
Please direct all Galaxy development questions to the -dev list (cc'd); this
ensures that they get answered quickly and by the right people.
> i will put it in the toolshed. I had a few additional questions in the
> Issue-Tracker, but unfortunately i can't access it. Is that intentional?
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 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 S3 server
> from
Hi Derrick,
Yes, this approach will work fine.
Greg Von Kuster
On Oct 8, 2012, at 11:44 PM, Derrick Lin wrote:
> Can I actually just skip executing the migration script, and just install BWA
> from the tool shed like I did for other shed tools?? Should be fine I guess?
>
> Derrick
>
> On Tue
Hi Derrick,
This behavior is likely the result of your not having any entries for the bwa
tools defined in your tool_conf.xml file. Your tool_conf.xml file is parsed as
a part of the process of installing the migrated tools in order to load your
tool panel in the same way it was defined before
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