Hi all,
What if the input dataset selection for tools could be selected via
clicking a dataset (or even more) directly in the history, instead of
selecting from that good ol' dropdown box?
It is just that I have to concatenate the contents of 24 files... I
agree, in bash the command is
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the BAM is displayed nicely):
[ti_index_core] bug in BGZF: 80048ed5001b 80048ed5
Thanks for any input,
Joachim
--
Joachim
Here are the links to get the gff and the related genome files:
http://genomeportal.jgi-psf.org/Crypa2/download/Cparasiticav2.GeneCatalog20091217.gff.gz
http://genomeportal.jgi-psf.org/Crypa2/download/Cryphonectria_parasiticav2.nuclearAssembly.unmasked.gz
Whatever the file type I set for the
Not exactly what you asked for but it would allow you to build tools to
solve this problem and I never pass up an opportunity to sell my pull
requests:
https://bitbucket.org/galaxy/galaxy-central/pull-request/76/multi-input-data-tool-parameter-fixes
This would allow one to put a multiple=true on
On Oct 24, 2012, at 3:36 AM, Joachim Jacob joachim.ja...@vib.be wrote:
PS: I would have posted on Trello, but I am not allowed to do so. I
understand that this is the way to propose enhancements.
For adding cards, anyone can use the form at http://galaxyproject.org/trello.
A new card will be
Thanks for this Trello. Looks nice and powerful! it would be great to
have more Trello lists, like: enhancements requests, Currently working
on, ... etc.
I love to help sorting the trello lists, but we cannot drag en drop the
cards around. A last comment ( ^_^ ) it is rather cumbersome to start
Can you please share the datasets that are generating this errors?
Thanks,
J.
On Oct 24, 2012, at 4:19 AM, Joachim Jacob wrote:
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the
Passing it back to Jeremy, there is also a Javascript wrapper around the
tools API which might help:
https://bitbucket.org/galaxy/galaxy-central/src/tip/static/scripts/mvc/tools.js
Yes, the Galaxy team is working on a JavaScript binding to the API, and one of
the areas that we've done some
Hi John,
+1 Will it be accepted in galaxy-central? This looks very useful to me.
Cheers,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 10/24/2012 01:41 PM, John Chilton
Hello,
Recently I started 2 local galaxy servers on Linux PC for internal use. I
noticed that the main WSGI process uses a lot of CPU time - see the output
of ps command below:
$ ps aux | head -1 ps aux | grep wsgi
[1] 5293
USER PID %CPU %MEMVSZ RSS TTY STAT START
On Oct 20, 2012, at 10:36 AM, Christos Kannas wrote:
Hi all,
We have a locally installed Galaxy server that runs only a set of tools we
are developing.
It has been setup to run with 3 Web processes , 1 Job Manager and 4 Job
Handlers.
This setup is beeing run behind an Apache web
Hi Nate,
I do not see anything in the manager.log that seems as a HTTP request.
All Galaxy processes are set to listen from localhost.
When I change this to 0.0.0.0 I can access manager process by requesting
http directly to its listening port.
To me it seems that this RewriteRule is somehow
On Oct 23, 2012, at 12:07 PM, lenta...@jimmy.harvard.edu wrote:
Hi,
We have some common admin-tasks that we would like to implement on our
instance, but before doing so, we were wondering what Galaxy has already
baked it.
1. Is the Galaxy team planning to implement job_walltime for the
Hello Peter,
Thanks very much for this - I'm sure many will find it very helpful. I've
applied your patch to changeset revision 8096:0c56502c7fd7, which will be
included in the next Galaxy release currently scheduled for next Friday (not
today's currently scheduled release).
Thanks again,
On Oct 23, 2012, at 12:55 PM, Anthonius deBoer wrote:
I created the index but that did not change anything...
I had sent James Taylor the schema as he requested, but I never heard
anything so I guess he must not have found anything weird...
I am waiting to move my Galaxy server off to a
On Wed, Oct 24, 2012 at 4:46 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
Thanks very much for this - I'm sure many will find it very helpful. I've
applied your patch to changeset revision 8096:0c56502c7fd7, which
will be included in the next Galaxy release currently scheduled for
Hi, Paul
I would like to know if mod_wsgi has been considered for the deployment of
Galaxy at all, and whether anyone has any positive or negative experiences
with it.
I can only speak for the second part of your question: I've had some
experience with Apache 2 + mod_wsgi, but within a Django
On 24/10/12 18:09, Carl Eberhard wrote:
I would like to know if mod_wsgi has been considered for the deployment of
Galaxy at all, and whether anyone has any positive or negative experiences with
it.
I can only speak for the second part of your question: I've had some
experience with Apache 2
Hello
We have some tools that wrap an in-house program which generates an
Excel spreadsheet as one of its outputs, and wanted Galaxy to associate
the correct mime type so that the user's browser knows how to handle it
on view/download.
The advice on the wiki at
The Galaxy application does store quite a bit in memory (not as
globals though). This doesn't preclude running under mod_wsgi, but it
will work best in a configuration that uses a small number of long
running processes with multiple threads.
Basically, we run nginx proxying paste on the main
Do the APIs produce the proper CORS headers? Access-Control-Allow-Origin:
*, and responding to OPTIONS requests would be enough. Since this is an
API protected by a key, this doesn't have any real security implications to
just have hard-coded in.
Rob
On Oct 23, 2012 9:59 PM, Brad Chapman
The galaxy webserver can solve this by allowing cross-domain resources from
whatever toolsheds have been configured.
http://en.wikipedia.org/wiki/Cross-origin_resource_sharing
-Joel
___
Please keep all
Hello Carlos,
The cause of the server error is a tool shed issue which I've corrected, so you
should now be able to install the gmap repository. I've installed the
repository locally and it seems to be ok (althoug I haven't executed contained
tools), but it's in a strange state in the tool
Hi David,
Setting the following in your community_wsgi.ini file should enable remote
authentication in the tool shed. Features like this that are available in
Galaxy itself are usually also available in the tool shed (and function the
same way) since the code base supporting the features is
The error you saw was generated by tabix (which is used for fast random access
to interval files), so it's possible that you hit tabix's upper bound. You
might consider following up with the tabix folks to see what the issue is.
As you noted, your dataset is definitely better formatted as a
FYI, trackster supports BigWig directly (no conversion or additional
indexing) and quite efficiently, so you will likely have the most luck
with that.
-- jt
On Wed, Oct 24, 2012 at 3:09 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
bigwig file.
On Oct 19, 2012, at 9:35 AM, Carlos Borroto carlos.borr...@gmail.com wrote:
On Fri, Oct 19, 2012 at 12:00 AM, Fields, Christopher J
cjfie...@illinois.edu wrote:
My local one is set up like this and it works (for augustus):
Hi Niel,
I'm assuming the data uploaded to a library on a galaxy cloudman instance.
In that case, all the data that's uploaded to a data library (or a history)
goes on an nfs-exported file system and is thus available to all the worker
nodes.
Cheers,
Enis
On Wed, Oct 24, 2012 at 3:51 PM,
Thanks for the information. Much appreciated
Neil
From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Thursday, 25 October 2012 7:38 AM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Importing files into Libraries
Hi Niel,
I'm assuming the
Hi,
I am having an issue withuploading data via FTP. I get the following
error:
Response:530 Sorry, the maximum number of clients (3) for this
user are already connected.
Error: Critical error
Error: Could not connect to server
Is this because I try to upload too many
Hi all,
After updating my galaxy-dist to the latest release (23/Oct) I get the
following error message when I try to access one of my data libraries.
Error attempting to display contents of library (testlibrary):
(OperationalError) no such column: True u'SELECT dataset_permissions.id AS
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