-- Forwarded message --
From: hari krishna
Date: Tue, Apr 12, 2011 at 11:57 AM
Subject: configuration of reports at galaxy
To: galaxy-dev@lists.bx.psu.edu
Hi,
hi can any one explain how can i get reports per tool option in galaxy,
I tried by configurating reports_wsgi.i
James Taylor wrote, On 04/11/2011 09:05 PM:
> Assaf, it should be the last modification to the dataset's metadata, info,
> etc. Any change that would be made through the edit attributes page.
>
> I agree this is confusing and should probably not be shown to the user at all.
>
> On Apr 11, 2011,
Assaf, it should be the last modification to the dataset's metadata,
info, etc. Any change that would be made through the edit attributes
page.
I agree this is confusing and should probably not be shown to the user
at all.
On Apr 11, 2011, at 7:13 PM, Assaf Gordon wrote:
It doesn't give
Hi,
Kudos on the new "View Details" button implementation, both visually nice and
less intrusive tooltips.
However, you know me - I can't just give praise without complaining...
1. The "View Details" tooltip (the actual tooltip) is not using JQuery, so the
yellow (browser native) tooltip is sh
Hi Liisa,
What does "hg tip" return?
K
On Mon, Apr 11, 2011 at 10:55 AM, Liisa Koski
wrote:
> Hi I just tried to update my local installation of Galaxy but accidentally
> hit Ctr-C when it asked me a question
>
> added 285 changesets with 649 changes to 354 files
> local changed static/script
I screwed Galaxy. I will delete / reinstall it. At least I will delete
it. I think I will revert back to the shell for awhile to get some work
done. I've spent *way* too much time trying to get galaxy to work
properly. Thanks for all the help everyone.
On 4/11/11 4:32 PM, Ryan Golhar wro
Yeah, I pulled down a new version of galaxy-dist to a new directory and
am comparing the differences using diff on my current instance. For
some reason hg pull -u didn't work. It aborted because I installed a
bam.xml for igv in display_applications/igv. Apparently one was added
to galaxy-dis
Hi Ryan,
I still think it's a javascript problem (most of the fancy DHTML tricks in
galaxy, like expanding/collapsing datasets, are done in javascript - so when
something like that doesn't work, it's a good place to start).
First indication:
If you go to your galaxy server with Firefox and open
I restarted the galaxy daemon, apache, and cleared my cache. Still
didn't help. I'd be happy to share the URL of my instance via private
email if it'll help.
On 4/11/11 3:05 PM, Assaf Gordon wrote:
Couple of voodoo things to try:
1. Manually clean the cache of your web browser
2. Restart yo
Couple of voodoo things to try:
1. Manually clean the cache of your web browser
2. Restart your apache/nginx
Depending on your last update revision, it's possible that some of your
javascripts were updated by the latest pull, but your webbrowser maintains a
cached older version.
Those are the t
Second problem...Galaxy no longer can determine when a job completes in
PBS. I see it submit the job and the paster.log indicates the job ends,
but the history display indicates the job hasn't been submitted.
On 4/11/11 2:43 PM, Ryan Golhar wrote:
This happens in Firefox on Mac as well.
On
This happens in Firefox on Mac as well.
On 4/11/11 2:36 PM, Ryan Golhar wrote:
This is Safari on Mac OS X. I just reverted to my backup and the problem
still exists so I don't know what is going on now.
On 4/11/11 2:35 PM, Peter Cock wrote:
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar wrote:
This is Safari on Mac OS X. I just reverted to my backup and the
problem still exists so I don't know what is going on now.
On 4/11/11 2:35 PM, Peter Cock wrote:
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar wrote:
I just updated my local galaxy instance using hg pull, and the history items
a
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar wrote:
> I just updated my local galaxy instance using hg pull, and the history items
> are no longer expandable. What happened?
Which browser(s) are affected? I recall reporting some issues
with Internet Explorer only and the history peep view not wo
I just updated my local galaxy instance using hg pull, and the history
items are no longer expandable. What happened?
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Thanks for the quick answer,
Jeremy Goecks wrote, On 04/11/2011 12:50 PM:
>
>> Assuming cuffcompare generates a TMAP and REFMAP file for each
>> input file, does this mean the wrapper tool retrieves only the
>> first and second input files' TMAP and REFMAP files ?
>
> Yes, this is the way it wor
Assaf,
Assuming cuffcompare generates a TMAP and REFMAP file for each input
file, does this mean the wrapper tool retrieves only the first and
second input files' TMAP and REFMAP files ?
Yes, this is the way it works currently. This is clearly problematic,
but it meets most users' needs a
In my local instance of Galaxy, I'm trying to download the BAM and BAI
file from the tool SAM-to-BAM. I see the links for downloading the
Dataset and bam_index.
BTW - I'm running Safari on Mac OS X.
When I download the Dataset, I get the BAM file. When I download the
bam_index, it gets rena
Hello Peter,
Thanks for reporting this - it has been corrected within the tool shed.
Greg Von Kuster
On Apr 5, 2011, at 11:50 AM, Peter Cock wrote:
> Hi all,
>
> I had wondered why none of the tools on the Galaxy Tool Shed had a
> rating, and had assumed it was just that so far no-one had both
Hello,
I'm trying to write my own wrappers for Cufflinks,Cuffcompare,Cuffdiff,
learning mostly by looking at the existing tools.
I have a question regarding the multiple input/output implementation in
CuffCompare:
In CuffCompare, the XML can accept multiple input files (with a ), and
the sect
Hi I just tried to update my local installation of Galaxy but accidentally
hit Ctr-C when it asked me a question
added 285 changesets with 649 changes to 354 files
local changed static/scripts/packed/jquery.jstore.js which remote deleted
use (c)hanged version or (d)elete? interrupted!
When I t
Dear Vincent:
We do not currently have a Stampy wrapper, but this has been suggested by many
as an excellent alternative to our exiting mappers. Please go ahead with
wrapping it and share your code through Galaxy tool shed @
http://usegalaxy.org/community
Thanks!
anton
galaxy team
On Apr 11,
Hello everyone,
I would like to integrate Stampy
(http://www.well.ox.ac.uk/project-stampy) in Galaxy.
I couldn't find any wrapper available on the website.
If someone has written a stampy wrapper and would like to share it,
please contact me.
Thanks in advance for your help;
--
Vincent Le Tex
On Apr 8, 2011, at 11:01 AM, Dave Walton wrote:
> This is very close to our config, except -
> We run all of this on a 4 core Virtual Machine running SUSE Linux Enterprise
> Server 11 (x86_64) with 16 GB of memory.
>
> Instead of SGE our HPC cluster uses Torque/Moab for scheduling.
>
> Also, we
Hello everyone
I finally managed to finish my two scripts. It's kind of dirty coded
(I'm not a Perl fan + I was in a hurry), but at least they worked for
me. I could successfully transfer the data from an old MySQL Galaxy to
my new PSQL Galaxy.
Before running the scripts, you should already have
Hello everybody,
i'm in the process to provide Galaxy for multiple team. I've already
setup a testing instance using the production setup page on the wiki
(apache + sge) and it works quite well if i'm refearing to the users
feedback. This setup is typically use for NGS dealing with data on a NFS
s
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