[galaxy-dev] Local Galaxy Apache Config

2014-11-20 Thread Nicholas Kline
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

Re: [galaxy-dev] Local Galaxy web layout

2014-02-19 Thread sam guerler
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-dev] Local Galaxy web layout

2014-02-17 Thread shenw...@gmail.com
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

Re: [galaxy-dev] Local Galaxy web layout

2014-02-17 Thread Hans-Rudolf Hotz
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

Re: [galaxy-dev] Local Galaxy web layout

2014-02-17 Thread sam guerler
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,

[galaxy-dev] Local Galaxy Install - Debug Report FROM address as Admin and not User?

2013-10-01 Thread Adam Brenner
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

Re: [galaxy-dev] Local Galaxy Install - Debug Report FROM address as Admin and not User?

2013-10-01 Thread Martin Čech
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:

Re: [galaxy-dev] Local Galaxy Install - Debug Report FROM address as Admin and not User?

2013-10-01 Thread Adam Brenner
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

Re: [galaxy-dev] Local Galaxy Install - Debug Report FROM address as Admin and not User?

2013-10-01 Thread Martin Čech
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

Re: [galaxy-dev] Local Galaxy Install - Multiple Input Files for Workflow Missing?

2013-09-25 Thread Dannon Baker
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

[galaxy-dev] Local Galaxy Install - Multiple Input Files for Workflow Missing?

2013-09-24 Thread Adam Brenner
Howdy, On our local galaxy cluster, I have gotten a report that the multiple input files selection on workflows is missing. How do I enable it? Looking at the past mailing list[1] this is the item that is missing from our setup -- the tooltip icon. We are running a version of galaxy that is

Re: [galaxy-dev] Local Galaxy Install - Multiple Job Handlers - Uploads waiting to run endlessly

2013-04-16 Thread Adam Brenner
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

Re: [galaxy-dev] Local Galaxy Install - Multiple Job Handlers - Uploads waiting to run endlessly

2013-04-14 Thread Adam Brenner
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

[galaxy-dev] Local Galaxy Install - Multiple Job Handlers - Uploads waiting to run endlessly

2013-04-11 Thread Adam Brenner
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

Re: [galaxy-dev] Local Galaxy Install - Multiple Job Handlers - Uploads waiting to run endlessly

2013-04-11 Thread Adam Brenner
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 -

[galaxy-dev] local galaxy tool shed install

2013-01-15 Thread mark.rose
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

Re: [galaxy-dev] local galaxy tool shed install

2013-01-15 Thread Greg Von Kuster
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

[galaxy-dev] Local galaxy

2012-12-13 Thread Jennifer Jackson
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

Re: [galaxy-dev] Local galaxy

2012-12-13 Thread Jeremy Goecks
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

Re: [galaxy-dev] Local Galaxy concept system: hardware spec

2012-08-14 Thread Paul-Michael Agapow
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

Re: [galaxy-dev] Local Galaxy concept system: hardware spec questions

2012-08-14 Thread Sebastian Schaaf
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

[galaxy-dev] Local Galaxy concept system: hardware spec questions

2012-08-13 Thread Sebastian Schaaf
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 of tools and workflows (using Galaxy, sure) as well as platform for some alpha users, who

Re: [galaxy-dev] Local Galaxy concept system: hardware spec questions

2012-08-13 Thread Peter Cock
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

Re: [galaxy-dev] Local Galaxy concept system: hardware spec questions

2012-08-13 Thread Sebastian Schaaf
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

Re: [galaxy-dev] Local Galaxy concept system: hardware spec questions

2012-08-13 Thread Scott McManus
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

[galaxy-dev] Local galaxy cannot connect to local toolshed

2012-03-28 Thread Joachim Jacob
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

Re: [galaxy-dev] Local galaxy Cufflinks problem

2011-11-16 Thread Jeremy Goecks
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.

[galaxy-dev] Local galaxy Cufflinks problem

2011-11-11 Thread Bidwell, Christopher A.
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

Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-11-03 Thread Mickael ESCUDERO
-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

Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-11-02 Thread Nate Coraor
as output. If I run 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

Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-11-02 Thread Jerico Nico De Leon Revote
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

[galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-31 Thread Mickael ESCUDERO
@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

Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-27 Thread Nate Coraor
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

[galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-26 Thread Jerico Nico De Leon Revote
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

Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-26 Thread Jerico Nico De Leon Revote
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

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Anton Nekrutenko
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

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Hans-Rudolf Hotz
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').

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Nate Coraor
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,

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-18 Thread Nate Coraor
Tena Sakai wrote: Hi Nate, I am still not there, though I am getting closer... I changed the port to in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG

Re: [galaxy-dev] local galaxy display problem

2011-02-18 Thread Nate Coraor
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

Re: [galaxy-dev] local galaxy display problem

2011-02-18 Thread Nate Coraor
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

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Nate Coraor
Tena Sakai wrote: Hi I am a developer for a group. I am having a problem with local installation of galaxy. The platform I am using is: $ uname -o GNU/Linux $ uname -i x86_64 $ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008 $ uname -r 2.6.9-78.0.1.ELsmp

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Nate Coraor
Nate Coraor wrote: $ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008 $ uname -r 2.6.9-78.0.1.ELsmp RHEL 4, I believe? $ cd galaxy-dist $ sh run.sh ...lots of lines here... Fetch successful. ...more lines here... ysam/csamtools.py, line 6, in

[galaxy-dev] local galaxy display problem

2011-02-17 Thread Ryan Golhar
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

Re: [galaxy-dev] local galaxy display problem

2011-02-17 Thread Nate Coraor
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

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Tena Sakai
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

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Nate Coraor
Tena Sakai wrote: 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

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Tena Sakai
Hi Nate, I am still not there, though I am getting closer... I changed the port to in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Ross
The output:  Starting server in PID 28721.  serving on http://127.0.0.1: means that you have configured Galaxy to ONLY listen for connections from the server (localhost) itself so it will refuse connections from other machines. If you change 127.0.0.1 to 0.0.0.0 in universe_wsgi.ini and

Re: [galaxy-dev] local galaxy display problem

2011-02-17 Thread Ryan Golhar
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 Galaxy

Re: [galaxy-dev] local galaxy display problem

2011-02-17 Thread Ryan Golhar
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

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Tena Sakai
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: