Hello Galaxy Admins,
I am attempting to setup a local production-grade Galaxy server for
our department. Before I go ahead and turn on Galaxy for the first
time, would you be so kind as to please review my Apache2 config files
for errors? I want to be sure that things are in the correct place to
local Galaxy.As a
result,would you please show me some more details about this?
Regards, Shenwiyn
*From:* sam guerler aysam.guer...@gmail.com
*Date:* 2014-02-18 01:20
*To:* Hans-Rudolf Hotz h...@fmi.ch
*CC:* shenw...@gmail.com; galaxy-dev galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev
Galaxy developers:I want to change my local Galaxy web layout,for
example,delete the top button of Visualization and Cloud or change their
positions.Could anyone show me some details about this?Thank you very much.
shenw...@gmail.com
Hi Shenwiyn
Have a look at:
~/galaxy_dist/database/compiled_templates/base_panels.mako.py
Regards, Hans-Rudolf
On 02/17/2014 08:04 AM, shenw...@gmail.com wrote:
Galaxy developers:
I want to change my local Galaxy web layout,for example,delete the top
button of Visualization and Cloud or
Hi Shenwiyn,
This has changed recently. Please take a look at:
static/scripts/galaxy.menu.js
Using that file, you can add/remove/change labels and their position. It is
recommended to run pack_scripts.py after changing the source file.
Regards, Sam
On Mon, Feb 17, 2014 at 11:33 AM,
Howdy,
On our local Galaxy install, everytime a user submits a bug report, it
does email all the admins -- as defined in universe_wsgi.ini -- but
the FROM address is not of the user, but rather the first email
address from the admin list.
Is this normal? May we have it changed so the FROM
Hi Adam,
you are right about the behaviour, this is what Galaxy does. However it
sends the email to the user too, so Reply all will reach the user's email
address. This is how the feature was meant to be used.
Martin
On Tue, Oct 1, 2013 at 12:59 PM, Adam Brenner aebre...@uci.edu wrote:
Martin,
Thanks for the response. Yes, I do notice the reply-to address does
include the user, but wouldn't it be better if the FROM address was
from the actual user reporting the error? When checking my email, for
example, I do not want to see emails that are FROM me, to MYSELF when
its really
Adam,
it is function *report_error* in
/lib/galaxy/webapps/galaxy/controllers/dataset.py
you need to set this line
* frm = to_address
* to
* frm = email*
and you should be all set.
Martin
On Tue, Oct 1, 2013 at 2:12 PM, Adam Brenner aebre...@uci.edu wrote:
Martin,
Thanks for the
Are you using Input Dataset steps in your workflows? The multiple inputs
feature uses these to know how to distribute inputs -- other than that no
other configuration steps are necessary.
On Tue, Sep 24, 2013 at 2:43 PM, Adam Brenner aebre...@uci.edu wrote:
Howdy,
On our local galaxy
So I finally figured it out (thanks to the help from the IRC folks, bag and
natefoo).
I incorrectly had my job_conf.xml setup where no job runners were set. All
is working now.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Anyone have any ideas? Still have not sorted this out
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
Howdy Galaxy Admins,
I am installing Galaxy on our HPC cluster and running into a strange issue
that I can no longer debug further. I am running the latest galaxy build as
of Tuesday April 9th.
hg clone https://bitbucket.org/galaxy/galaxy-dist/
hg update stable
When a user tries to
FYI: Here are the entries in paster.log. If you notice no job_handlers are
being sent. I performed tests on both nginx reverse proxy and direct
localhost:8080 (limited to our private network on campus)
128.200.34.227 - - [11/Apr/2013:13:24:40 -0700] GET
/tool_runner?tool_id=upload1 HTTP/1.0 200 -
Having followed the directions in HostingALocalToolShed I ran
run_community.sh with the default configurations in community_wsgi.ini. It
executed without error but failed to start the tool shed as
http://127.0.0.1:9009 returns Unable to Connect error
Thanks for your help
Mark
This
Hi Mark,
What version of Galaxy are you running, and what does your tool shed paster log
show?
Greg Von Kuster
On Jan 15, 2013, at 5:49 PM, mark.r...@syngenta.com wrote:
Having followed the directions in “HostingALocalToolShed” I ran
run_community.sh with the default configurations in
Repost to mailing list
___
For discussion of local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi
I am doing NGS analysis in our local galaxy, I
Hi
I am doing NGS analysis in our local galaxy, I would like to access the
output files for further analysis.
I do have an account on the server where galaxy is installed, so I would like
to access the output files without actually downloading them( aince they are
huge). Can you
Some quick answers in the hopes that more qualified people will chip in:
I have a couple of question around the topic hardware requirements
for
a server which is intended to be bought and used as concept machine for
NGS-related jobs.
First a comment - it sounds a bit
Hey Scott,
First of all thanks for the long reply - to keep it short I'll follow
you with answering inline:
Scott McManus wrote:
Hey Sebastian-
It may help to consider other pieces aside from compute nodes
that you will need, such as nodes for proxies and databases,
networking gear (such
On Mon, Aug 13, 2012 at 11:23 AM, Sebastian Schaaf
sch...@ibe.med.uni-muenchen.de wrote:
Hi all,
I have a couple of question around the topic hardware requirements for a
server which is intended to be bought and used as concept machine for
NGS-related jobs. It should be used for development
Yes, thanks, I should have mentioned that.
I posted in both forum and dev-list, because I don't expect the forum
members and the dev-list subscribers to be a 100% identical...
Sorry for any inconvenience...
Peter Cock wrote:
On Mon, Aug 13, 2012 at 11:23 AM, Sebastian Schaaf
Hey Sebastian-
It may help to consider other pieces aside from compute nodes
that you will need, such as nodes for proxies and databases,
networking gear (such as switches and cables), and so on.
http://usegalaxy.org/production has some details, and there are
high-level pieces explained at
Hi,
I managed to run a local Tool Shed and add a repository.
On the same machine, a local galaxy is running, and configured for using
this local toolshed.
In the Admin menu of Galaxy, I can see my local Toolshed listed under
'Search and Browse tool sheds'.
However, when I click on my
Chris,
The problem is likely a bug in the Cufflinks wrapper that was recently fixed in
galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60
Try updating your Galaxy instance to include this changeset; if this doesn't
fix the problem, let us know.
Good luck,
J.
Colleagues,
We have set up a local Galaxy but I am having trouble running Cufflinks with
the annotation gtf file. We have the iGenomes btau4.2 genome in the database
and use the iGenomes btau4.2 gtf file in the history. However the –G isn’t
showing up in the command line (below) and the
-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error
Message-ID:
cap9ulhyipxyb2cwtqosm3mquuu55arxy5por1dbahej1uco...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi,
I'm just doing a simple get-data from UCSC on our local
the same tools locally there is no problem.
Cheers
Micka
Message: 5
Date: Thu, 27 Oct 2011 15:08:17 +1100
From: Jerico Nico De Leon Revote jerico.rev...@monash.edu
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error
Message-ID
@lists.bx.psu.edu
Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error
Message-ID:
cap9ulhyipxyb2cwtqosm3mquuu55arxy5por1dbahej1uco...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi,
I'm just doing a simple get-data from UCSC on our local Galaxy
instance and got
Jerico Nico De Leon Revote wrote:
Hi,
I'm just doing a simple get-data from UCSC on our local Galaxy
instance and got the following error:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The job box then is displayed as red on the history panel.
The
Hi,
I'm just doing a simple get-data from UCSC on our local Galaxy
instance and got the following error:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The job box then is displayed as red on the history panel.
The job runner states that the job finished
Just to follow-up on this. The MarkupSafe egg is definitely present on the
eggs directory and the servers are ran through virtualenv.
On 27 October 2011 15:08, Jerico Nico De Leon Revote
jerico.rev...@monash.edu wrote:
Hi,
I'm just doing a simple get-data from UCSC on our local Galaxy
Lee:
I am CC'ing you e-mail to galaxy-dev list. You can get a lot of useful answers
by posting to this list. Maintaining Galaxy is not different from maintaining
other software resources. To run it locally you will need to have a system
administration supervision as with any other high
Hi Lee
* What is a realistic amount of someones time to implement Galaxy on a Linux
server so that it can be used by researchers using the Web?
Galaxy is simple to set up and works out-of-the-box. You will have a
functional Galaxy server within minutes (yes, 'within minutes').
Hi Lee,
If setting up Galaxy on an existing supported cluster, I would estimate
the setup time for an experienced sysadmin to be a day or two, although
that number can be larger if a lot of tools that depend on external
binaries (e.g. NGS mappers) and locally cached reference genomes are
desired,
Ryan Golhar wrote:
I've implemented the Serving Galaxy at a sub directory (such as
/galaxy), made the change to Apache, and the universe_wsgi.ini.
When I view the page through Apache using http://server.name/galaxy,
the page is garbled like something didn't take.
Hi Ryan,
Did you
Ryan Golhar wrote:
SOLVED. I copied/paste the Rewrite rules for apache from the wiki
without updating the paths to my installation...once I did that, all
worked well.
Whoops, I should read ahead before I reply. Glad it's working!
--nate
On 2/17/11 5:07 PM, Ryan Golhar wrote:
I've
I've set up a local instance of Galaxy following the instructions in the
wiki for a production instance. I'm running on CentOS with Apache, and
a mysql database server.
Everything looks great when viewed directly through the Galaxy web
server on port 8080.
I've implemented the Serving
Ryan Golhar wrote:
I've set up a local instance of Galaxy following the instructions in
the wiki for a production instance. I'm running on CentOS with
Apache, and a mysql database server.
Everything looks great when viewed directly through the Galaxy web
server on port 8080.
I've
Hi Nate,
Thank you for your reply.
I am getting there, but I need a bit more help.
Firstly, yes, I had an alias hg (which was history | grep $1).
I got rid of it and hg is working fine.
Secondly, I installed the latest version of zlib (1.2.5) and
I can go further with sh run.sh, but it hangs
SOLVED. I copied/paste the Rewrite rules for apache from the wiki
without updating the paths to my installation...once I did that, all
worked well.
On 2/17/11 5:07 PM, Ryan Golhar wrote:
I've set up a local instance of Galaxy following the instructions in
the wiki for a production
Hi Nate,
Please ignore my previous post. I got it working.
I changed an entry in universe_wsgi.ini file.
From #host = 127.0.0.1 to host = vixen.egcrc.org.
It appears to be working.
Many thanks for your help.
Regards,
Tena Sakai
On 2/17/11 1:48 PM, Tena Sakai tsa...@gallo.ucsf.edu wrote:
42 matches
Mail list logo
