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
...@jamestaylor.org
wrote:
Definitely not. And please keep replies on the list.
-- jt
On Fri, Sep 21, 2012 at 1:50 PM, Chebbi Mohamed Amine
chebbimam...@gmail.com wrote:
Yes the two instances are of two different versions. So if I
understand well
there is no mean to do it like this ?
Thanks
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
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 the latest one or no ?
Thanks
Amine
2012/7/20 Chebbi
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
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:
HI!
I'am usig Galaxy-dist.
SO I have done the test again, I did
. Are
there certain scenarios where Trackster/Galaxy is more likely to crash?
Finally, are you using galaxy-dist or galaxy-central?
Best,
J.
On Jul 18, 2012, at 8:50 AM, Chebbi Mohamed Amine wrote:
-- Forwarded message --
From: Chebbi Mohamed Amine chebbimam...@gmail.com
Date
-- Forwarded message --
From: Chebbi Mohamed Amine chebbimam...@gmail.com
Date: 2012/7/18
Subject: Re: [galaxy-dev] Galaxy crach while visualization
To: Jeremy Goecks jeremy.goe...@emory.edu
Hello Jeremy!
Thanks for your response. Yes the paster.log is not complaining. Excuse me
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 - -
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
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?
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 (display file=igv/bam.xml /). However the Links dose not
appear in bam history items. I see only display in IGB
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 chebbimam...@gmail.com
Hi !
I'am trying to set IGV as a display application in Galaxy. So I have addedin
datatypes_conf.xml, under the bam
Thanks !
2012/6/28 Edward Kirton eskir...@lbl.gov
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 !
I have to use the smtp-server in Galaxy
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
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 h...@fmi.ch
On 06/19/2012 07:11 PM, Chebbi Mohamed Amine
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 module
from galaxy
session.
Thank-you
Amine
2012/6/8 Nate Coraor n...@bx.psu.edu
On Jun 4, 2012, at 8:58 AM, CHEBBI Mohamed Amine wrote:
-- Forwarded message --
From: CHEBBI Mohamed Amine chebbimam...@gmail.com
Date: 2012/5/25
Subject: Proftpd Problem
To: galaxy-dev@lists.bx.psu.edu
-- Forwarded message --
From: CHEBBI Mohamed Amine chebbimam...@gmail.com
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
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
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:
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
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