Re: [galaxy-dev] Using an unique database for tow differents versions of Galaxy

t; > > On Fri, Sep 21, 2012 at 3:13 PM, James Taylor > wrote: > > Definitely not. And please keep replies on the list. > > > > -- jt > > > > > > On Fri, Sep 21, 2012 at 1:50 PM, Chebbi Mohamed Amine > > wrote: > > > Yes the two insta

[galaxy-dev] Using an unique database for tow differents versions of Galaxy

Hello Galaxy-team! I installed recently two differents versions of Galaxy and I would like to use the same database for the two instances without loosing data (histories, workflows etc..). Thank you in advance Amine ___ Please keep all repli

[galaxy-dev] Problem of running of galaxy

Hi Galaxy-team ! I have uploaded the latest version of Galaxy of 05/09. However when I run run.sh I have the message below and I haven't found how to fix that: "TypeError: Invalid argument(s) 'server_side_cursors' sent to create_engine(), using configuration SQLiteDialect/SingletonThreadPool/TLEn

[galaxy-dev] Galaxy-distribution (Nouvelle version)

Bonsoir, Une nouvelle version de Galaxy vient de sortir. D’après le Monsieur du maling list de Galaxy, les bugs de crash liés à l'utilisation du visualiseur Trackster devraient être résolus. Pourriez vous me dire vos recommandations à ce propos. Merci Amine

Re: [galaxy-dev] Galaxy crach while visualization

ast week that you > can update to: > > http://wiki.g2.bx.psu.edu/News > > Best, > J. > > On Jul 25, 2012, at 7:13 AM, Chebbi Mohamed Amine wrote: > > Hello Jeremy ! > Could you tell me how to find the version number of the current > galaxy-dist to know if I have t

Re: [galaxy-dev] Galaxy crach while visualization

Hello Jeremy ! Could you tell me how to find the version number of the current galaxy-dist to know if I have the latest one or no ? Thanks Amine 2012/7/20 Chebbi Mohamed Amine > Ok. Thanks for your clarifications. So I will wait for your upcoming > distribution of Galaxy and redo th

Re: [galaxy-dev] Galaxy crach while visualization

s that will > be available with the next distribution. > > If you're still experiencing problems after upgrading, let us know and > we'll keep trying to figure out what's going on. > > Best, > J. > > On Jul 19, 2012, at 11:03 AM, Chebbi Mohamed Amine wrote: &g

Re: [galaxy-dev] Galaxy crach while visualization

r. For Safari/Chrome, see the > View --> Developer --> JavaScript console option; for Firefox, see Tools > --> Web Developer --> Web Console. > > The fact that the Paster log isn't showing errors is problematic. Are > there certain scenarios where Trackster/Galaxy i

[galaxy-dev] Fwd: Galaxy crach while visualization

-- Forwarded message -- From: Chebbi Mohamed Amine Date: 2012/7/18 Subject: Re: [galaxy-dev] Galaxy crach while visualization To: Jeremy Goecks Hello Jeremy! Thanks for your response. Yes the paster.log is not complaining. Excuse me where I can found the javascript log. In /var

[galaxy-dev] Galaxy crach while visualization

Hello Galaxy team ! I have e strange problem whith my Galaxy trackster visualization . While viewing bookmarked regions in my visualisation the whole Galaxy process crashed and needed to be restarted, mainly when I use Chrome browser. Above the Paster.log : xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Ju

Re: [galaxy-dev] Byte-range support for IGV ?

like setting a JNLP file ? Thanks Amine 2012/7/11 Nate Coraor > On Jul 4, 2012, at 7:57 AM, Chebbi Mohamed Amine wrote: > > > HI Geert ! > > I did well : > > > > > > XSendFile on > > XSendFilePath / > > > > > &

[galaxy-dev] Display with IGV local

HI Galaxy-team ! I 'am trying to display BAM files whith the * local* IGV. However D*isplay with IGV "local*" use the already running copy of IGV on the server machine. So I need evry time to run manually igv by the command above: java -Xmx750m -jar igv.jar Is there any way to do this automatic

Re: [galaxy-dev] Byte-range support for IGV ?

> > best regards, > > Geert > > > On 07/04/2012 11:15 AM, Chebbi Mohamed Amine wrote: > > HELLO ! > > I just updated our local galaxy instance and just wanted to try the new > IGV display application. When I try to display a BAM file whith the local > IGV, I encou

[galaxy-dev] Byte-range support for IGV ?

HELLO ! I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message : "HTTP and FTP access to BAM files require byte-range support" Has anyone encountred the same probleme

Re: [galaxy-dev] Display IGV link within history bam items?

Resolved! In fact i forgot to set the database infomration (hg18) in the bam item. so Now I can see the display igv link :) 2012/7/3 Chebbi Mohamed Amine > Hi ! > I'am trying to set IGV as a display application in Galaxy. So I have addedin > datatypes_conf.xml, under the ba

[galaxy-dev] Display IGV link within history bam items?

Hi ! I'am trying to set IGV as a display application in Galaxy. So I have addedin datatypes_conf.xml, under the bam datatype the display application for igv/bam (). However the Links dose not appear in bam history items. I see only " display in IGB Local

Re: [galaxy-dev] Port Config SMTP Server

Thanks ! 2012/6/28 Edward Kirton > in the universe_wsgi.ini file, define the server:port like thus: > > smtp_server = smtp.gmail.com:587 > > On Thu, Jun 21, 2012 at 3:23 PM, CHEBBI Mohamed Amine < > am...@abgenomica.com> wrote: > >> Hi Galxy-team ! >>

[galaxy-dev] Port Config SMTP Server

Hi Galxy-team ! I have to use the smtp-server in Galaxy. However I don't see how to set the port to 587 in the universe_wsgi.ini to enable sending mails from my own server. I saw the documetation but I didn't find any response for this. Thank-you in advance for your help. Regards Amine

Re: [galaxy-dev] No module named galaxy !!

Hi Hans-Rudolf; Yes!! I didn't pay attention and i was really calling the script fom ~/galaxy_dist/scripts/cleanup_datasets/. Now when I call it from ~/galaxy_dist/ it works very well. Thanks :) Amine 2012/6/20 Hans-Rudolf Hotz > > > On 06/19/2012 07:11 PM, Chebbi Moham

[galaxy-dev] No module named galaxy !!

Hi Galaxy team ! I'am trying to remove userless histories from my galaxy database as mentoned in this link ( by using the command above : python cleanup_datasets.py universe_wsgi.ini -d 60 -1 However I get an error message like this : File "cleanup_datasets.py", line 13, in from galaxy impor

Re: [galaxy-dev] Proftpd Problem

session. Thank-you Amine 2012/6/8 Nate Coraor > On Jun 4, 2012, at 8:58 AM, CHEBBI Mohamed Amine wrote: > > > > > > > -- Forwarded message ------ > > From: CHEBBI Mohamed Amine > > Date: 2012/5/25 > > Subject: Proftpd Problem > >

[galaxy-dev] Fwd: Proftpd Problem

-- Forwarded message -- From: CHEBBI Mohamed Amine Date: 2012/5/25 Subject: Proftpd Problem To: galaxy-dev@lists.bx.psu.edu Hi, I'am trying to set up ProFTP on Debain to enable FTP upload on Galaxy installed locally? I followed the instructions on this link ( http://wi

[galaxy-dev] BWA Problem

Hi ! I have a problem when i execute BWA from my local galaxy instance. I have this error message : An error occurred running this job:*BWA Version: 0.6.1-r104 Error indexing reference sequence. [bwa_index] Pack FASTA... 2.35 sec [bwa_index] Construct BWT for the packed sequence... Segmentation fa

[galaxy-dev] Proftpd Problem

Hi, I'am trying to set up ProFTP on Debain to enable FTP upload on Galaxy installed locally? I followed the instructions on this link ( http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't work. When I restart proftpd i get this message : mod_tls_memcache/0.1: notice: unable

Re: [galaxy-dev] Running Galaxy behind apache2

Yes Carlos ! it's working now. Muchas Gracias :) 2012/5/14 Carlos Borroto > On Thu, May 10, 2012 at 4:23 PM, CHEBBI Mohamed Amine > wrote: > > I configured the apache2.conf like above : > > If you are using Ubuntu or Debian, the place to put this configuration > is &#x

[galaxy-dev] Fwd: Running Galaxy behind apache2

-- Forwarded message -- From: CHEBBI Mohamed Amine Date: 2012/5/11 Subject: Re: [galaxy-dev] Running Galaxy behind apache2 To: Nate Coraor Hi! When I go to http:// it displays: It works! This is the default web page for this server. The web server software is running but no

[galaxy-dev] Running Galaxy in a production environment

Hi Galaxy Team, I'am trying to put Galaxy into production on a dedicated server. And I have some questions please : 1) how can I integrate galaxy behind an Apache server (or nginx)? 2) how to switch the SQL lite database to the Postgresql one (would you have an example to do it)? 3) What shou