Hi
As part of my upgrade/testing work, I am looking at the visualization
plugins.
In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts',
'Scatterplot', and 'Trackster') seem to work fine.
All I have done was:
- I defined the visualization_plugins_directory in the
univ
Hi all,
I'm implementing a tool for our local galaxy instance which has multiple output
datasets.
The number of datasets are determined by the input so I've been following the
instructions at the bottom of this page:
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files.
As I un
It does works for me if I do exactly as described on that page
without using the universe_wsgi.ini option:
- I have the "force_history_refresh"
- I follow the exact file-name structure
(primary__somename_visible_filetype)
- I save the files in the dir from passed param
$__new_file_path__
Ca
Hi Stef,
I always restart galaxy and have done the other parts correct as well, but with
no luck.
In my universe_wsgi.ini file I have:
new_file_path = my/file/path
collect_outputs_from = new_file_path, job_working_directory
Does this look familiar?
Martin
From: stefvanliesh...@fastmail.fm
To
I do not use "new_file_path" and "collect_outputs_from" in
universe_wsgi.ini
In my tool code I directly save to files to:
$__new_file_path__/primary__somename_visible_filetype
As they say on the page:
To use this method at least one output dataset (output1 in our
example) must be specified
I went back to not using the options in the .ini file, but it still doesn't
work.
How to you specify $__new_file_path__? Or do you just enter the path in the xml
command line?
Martin
From: stefvanliesh...@fastmail.fm
To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
Subject: Re:
In the example they provide it to the sh tool:
example_tool.sh $input1 $output1 $output1.id $__new_file_path__
...so then the 3rd and 4th variables given to example_tool.sh
contain the and the output directory path. Save all the
extra output files to that directory with the exact format:
p
Hi, Hans,
What was the datatype (listed as 'format') of the dataset you tested with
here?:
> However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops
> up (instead of just "Visualize")
Trackster by default accepts all datatypes (all subclasses inheriting
data.Data) and is the
(oops, to continue the truncated sentence in the prev. email):
You can change that by editing the ...
config/trackster.xml 'datatype' as you did in your email to restrict what
Trackster can run on.
(sorry about that)
On Wed, Aug 27, 2014 at 9:39 AM, Carl Eberhard
wrote:
> Hi, Hans,
>
> What w
It still doesn't work. I see the files in the folder, but they don't show in
galaxy.
My command line looks like this:
myTool.sh $input1 $output1 $output2 546 /my/file/path/
Martin
From: stefvanliesh...@fastmail.fm
To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
Subject: Re: [ga
Follow the Galaxy wiki
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User
setup permission instructions.
Follow these 2 steps to get Galaxy to run as real users with IBM Platform
LSF:
Step 1) Download the latest LSF DRMAA 1.1.1 from github.
htt
Dont use "$output2", "546" and "/my/file/path/".
Do exactly this: myTool.sh $input1 $output1 $output1.id
$__new_file_path__
And then use the variables in your script ("$output.id" will
provide you with eg "546" and "$__new_file_path__" with the
output path)
Stef
- Original message -
But where are the variables defined then?
Martin
From: stefvanliesh...@fastmail.fm
To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Multiple output datasets
Date: Wed, 27 Aug 2014 16:11:49 +0200
Dont use "$output2", "546" and "/my/file/path/".
D
I guess that...
$output1 you have (hopefully) defined in your
section, and with ".id" you get the internal galaxy id of that
object.
And $__new_file_path__ is created by galaxy at execution of the
tool.
- Original message -
From: Martin Christiansen <[1]martinchristianse...@hot
Hi,
I'm trying to get a wrapper from someone else working and I found this
"refresh_on_change" attribute in his select boxes which are filled using the
dynamic_options feature:
...
When searching the documentation/wiki I do not find a reference to this, but it
would be a nice option
Hello all,
My users are trying to use a tool called bismark and it requires an unsorted
SAM file for one of its steps
Previous steps produce BAM files so we would like to include the tool
BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort
by default and there is no w
Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.
Peter
On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott
wrote:
> Hello all,
>
> My users are trying to use a tool called bismark and it requires an unsorted
> SAM file for one of its steps
>
> Previous st
I guess that is my point .. at a command prompt that can be achieved ( and
gives the result they need ) but as far as I can see the same is not true via
the Galaxy GUI ( unless there is a tool I am missing)
They have 96 separate files to process hence the desire to use a workflow.
Regards,
Ali
Ah - I missed this was on the Galaxy list, sorry.
I think that Galaxy automatically coordinate sorts "bam" files,
which is generally a good thing bar cases like yours. This
problem has undoubtedly come up before - an "unsortedbam"
datatype may be needed...
Peter
On Thu, Aug 28, 2014 at 1:35 PM,
19 matches
Mail list logo
