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

[Chebbi Mohamed Amine]

So in this case how is it possible to migrate data form  the old database
to the new one. In fact i have two different versions of Galaxy installed
in my machine and I don't want to loose data like histories that I creted
in the old version one.
Thanks for help

Amine

2012/9/21 Dannon Baker 

> The main problem with different versions of galaxy is that the database
> schema that they expect (as applied by versioned migrations from the galaxy
> codebase) is different.  So you could end up working with a database that
> has fields and keys you aren't expecting, which would be bad.
>
> -Dannon
>
> On Sep 21, 2012, at 3:54 PM, Promita Bose  wrote:
>
> > Perhaps I missed it but why 'Definitely not' ?
> > If storage is a limiting factor/constraint, then may be worth attempting
> ... ?
> >
> >
> > Promita
> >
> > 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 instances are of two different versions. So if I
> understand well
> > > there is no mean to do it like this ?
> > > Thanks
> > >
> > >
> > > 2012/9/21 James Taylor 
> > >>
> > >> If the two different Galaxy instances are different *versions* of
> > >> Galaxy, this is unlikely to work out well.
> > >>
> > >> -- jt
> > >>
> > >>
> > >> On Fri, Sep 21, 2012 at 11:59 AM, Chebbi Mohamed Amine
> > >>  wrote:
> > >> > 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 replies on the list by using "reply all"
> > >> > in your mail client.  To manage your subscriptions to this
> > >> > and other Galaxy lists, please use the interface at:
> > >> >
> > >> >   http://lists.bx.psu.edu/
> > >
> > >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >   http://lists.bx.psu.edu/
> >
> >
> >
> > --
> > MSc  Promita  Bose
> >   404-408-9060
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
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[galaxy-dev] Using an unique database for tow differents versions of Galaxy

[Chebbi Mohamed Amine]

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
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[galaxy-dev] Problem of running of galaxy

[Chebbi Mohamed Amine]

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/TLEngine.  Please check that the keyword
arguments are appropriate for this combination of components."

Thank you in advance
Amine
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[galaxy-dev] Galaxy-distribution (Nouvelle version)

[CHEBBI Mohamed Amine]

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
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Re: [galaxy-dev] Galaxy crach while visualization

[Chebbi Mohamed Amine]

Ok Jeremy ; So I will test the latest release.
Thanks
Amine

2012/7/25 Jeremy Goecks 

> Assuming that you're using Mercurial, which is highly recommended, you can
> type this at the command line:
>
> % hg tip
>
> You probably know that we released a new distribution last 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 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 the test.
>>
>> Best,
>> Amine
>>
>>
>> 2012/7/20 Jeremy Goecks 
>>
>>> Hmm, this appears to be an indexing error, but there are many potential
>>> causes so that doesn't narrow down the issue much.
>>>
>>> Because you're using galaxy-dist, the simplest thing to do is wait for
>>> our upcoming distribution (which should happen in the next couple days),
>>> upgrade and see if that fixes the problem. Trackster is under active
>>> development, so there are quite a few bug fixes and improvements 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 a simple scrolling to visualize by
>>> the Trackster the different  chromosome regions and then the galaxy crashed
>>> suddenly.
>>>
>>> Here Above what java script log looks :
>>>
>>> 22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5DFailed
>>> to load resource
>>>
>>> http://xxx.x.com/tracks/data?chrom=chr19&low=1449105&high=1449853&mode=Pack&resolution=1.8693312836279785&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5DFailedto
>>>  load resource
>>>
>>> However The paster.log looks more talking this time :
>>>
>>> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
>>> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=2a8867ca0da68ac1&hda_ldda=hda&filter_cols=%5B%22Score%22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5D
>>> HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
>>> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
>>> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
>>> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
>>> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Auto&resolution=2.3339731285988483&dataset_id=18644201db609b11&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>>> HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
>>> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
>>> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
>>> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
>>> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
>>> HTTP/1.1" 500 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
>>> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
>>> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
>>> Error - : could not open index
>>> `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat`
>>>
>>>
>>> 2012/7/19 Jeremy Goecks 
>>>
>>>> JavaScript logs are found in the Web browser. 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. A

Re: [galaxy-dev] Galaxy crach while visualization

[Chebbi Mohamed Amine]

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 the test.
>
> Best,
> Amine
>
>
> 2012/7/20 Jeremy Goecks 
>
>> Hmm, this appears to be an indexing error, but there are many potential
>> causes so that doesn't narrow down the issue much.
>>
>> Because you're using galaxy-dist, the simplest thing to do is wait for
>> our upcoming distribution (which should happen in the next couple days),
>> upgrade and see if that fixes the problem. Trackster is under active
>> development, so there are quite a few bug fixes and improvements 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 a simple scrolling to visualize by
>> the Trackster the different  chromosome regions and then the galaxy crashed
>> suddenly.
>>
>> Here Above what java script log looks :
>>
>> 22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5DFailed
>> to load resource
>>
>> http://xxx.x.com/tracks/data?chrom=chr19&low=1449105&high=1449853&mode=Pack&resolution=1.8693312836279785&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5DFailedto
>>  load resource
>>
>> However The paster.log looks more talking this time :
>>
>> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
>> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=2a8867ca0da68ac1&hda_ldda=hda&filter_cols=%5B%22Score%22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5D
>> HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
>> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
>> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
>> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
>> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Auto&resolution=2.3339731285988483&dataset_id=18644201db609b11&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>> HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
>> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
>> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
>> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
>> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
>> HTTP/1.1" 500 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
>> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
>> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
>> Error - : could not open index
>> `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat`
>>
>>
>> 2012/7/19 Jeremy Goecks 
>>
>>> JavaScript logs are found in the Web browser. 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 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 
>>> 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/log I haven't a

Re: [galaxy-dev] Galaxy crach while visualization

[Chebbi Mohamed Amine]

Ok. Thanks for your clarifications. So I will wait for your upcoming
distribution of Galaxy and redo the test.

Best,
Amine

2012/7/20 Jeremy Goecks 

> Hmm, this appears to be an indexing error, but there are many potential
> causes so that doesn't narrow down the issue much.
>
> Because you're using galaxy-dist, the simplest thing to do is wait for our
> upcoming distribution (which should happen in the next couple days),
> upgrade and see if that fixes the problem. Trackster is under active
> development, so there are quite a few bug fixes and improvements 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 a simple scrolling to visualize by
> the Trackster the different  chromosome regions and then the galaxy crashed
> suddenly.
>
> Here Above what java script log looks :
>
> 22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5DFailed
> to load resource
>
> http://xxx.x.com/tracks/data?chrom=chr19&low=1449105&high=1449853&mode=Pack&resolution=1.8693312836279785&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5DFailedto
>  load resource
>
> However The paster.log looks more talking this time :
>
> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=2a8867ca0da68ac1&hda_ldda=hda&filter_cols=%5B%22Score%22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5D
> HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Auto&resolution=2.3339731285988483&dataset_id=18644201db609b11&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
> HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
> HTTP/1.1" 500 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
> Error - : could not open index
> `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat`
>
>
> 2012/7/19 Jeremy Goecks 
>
>> JavaScript logs are found in the Web browser. 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 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 
>> 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/log I haven't any file
>> related to javascript.log.
>> Thanks
>> Amine
>>
>>
>> 2012/7/17 Jeremy Goecks 
>>
>>> Hello Amine,
>>>
>>> The paster log looks normal, and Postgre log is standard given the
>>> crash. Was there anything out of the ordinary that you can spot in the
>>> paster log and/or Javascript log in your Web browser?
>>>
>>> Thanks,
>>> J.
>>>
>>> On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote:
&g

Re: [galaxy-dev] Galaxy crach while visualization

[Chebbi Mohamed Amine]

HI!

I'am usig Galaxy-dist.

SO I have done the test again, I did a simple scrolling to visualize by the
Trackster the different  chromosome regions and then the galaxy crashed
suddenly.

Here Above what java script log looks :

22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5DFailed
to load resource
http://xxx.x.com/tracks/data?chrom=chr19&low=1449105&high=1449853&mode=Pack&resolution=1.8693312836279785&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5DFailedto
load resource

However The paster.log looks more talking this time :

xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
/tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=2a8867ca0da68ac1&hda_ldda=hda&filter_cols=%5B%22Score%22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5D
HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
/tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Auto&resolution=2.3339731285988483&dataset_id=18644201db609b11&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
HTTP/1.1" 200 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
/tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
HTTP/1.1" 500 - "http://..com/tracks/browser?id=df7a1f0c02a5b08e";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
Error - : could not open index
`/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat`


2012/7/19 Jeremy Goecks 

> JavaScript logs are found in the Web browser. 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 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 
> 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/log I haven't any file
> related to javascript.log.
> Thanks
> Amine
>
>
> 2012/7/17 Jeremy Goecks 
>
>> Hello Amine,
>>
>> The paster log looks normal, and Postgre log is standard given the crash.
>> Was there anything out of the ordinary that you can spot in the paster log
>> and/or Javascript log in your Web browser?
>>
>> Thanks,
>> J.
>>
>> On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote:
>>
>> 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/Jul/2012:12:56:36 +0200] "GET
>> /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>> HTTP/1.1" 200 - "
>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>> /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
>> HTTP/1.1" 200 - "
>> http://xxx.xxx.com/gala

[galaxy-dev] Fwd: Galaxy crach while visualization

[Chebbi Mohamed Amine]

-- 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/log I haven't any file
related to javascript.log.
Thanks
Amine


2012/7/17 Jeremy Goecks 

> Hello Amine,
>
> The paster log looks normal, and Postgre log is standard given the crash.
> Was there anything out of the ordinary that you can spot in the paster log
> and/or Javascript log in your Web browser?
>
> Thanks,
> J.
>
> On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote:
>
> 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/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1180427&high=1181609&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4)
> AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
> HTTP/1.1" 200 - "
> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] "GET
> /galaxy/tracks/data?chrom=chr19&low=814128&high=815310&mode=Auto&resolution=2.954022988505747&dataset_id=7710e7c5028

[galaxy-dev] Galaxy crach while visualization

[Chebbi Mohamed Amine]

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/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1180427&high=1181609&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4)
AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"
xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] "GET
/galaxy/tracks/data?chrom=chr19&low=814128&high=815310&mode=Auto&resolution=2.954022988505747&dataset_id=7710e7c5028b7c3b&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
HTTP/1.1" 200 - "
http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
like Gecko) Chrome/20.0.1132.47 Safari/536.11"

PostgreSQL saw the crach :

2012-07-12 12:56:40 CEST LOG:  could not receive data from client:
Connection reset by peer
2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:00:46.907
user=user database=database host=server port=33106
2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:03:45.206
user=user database=database host=server port=42867
2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:06:43.257
user=user database=database host=server port=56383
2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:04:22.120
user=user database=database host=server port=42663
2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:04:22.596
user=user database=database host=server port=42656


Thanks
Amine
___
Please keep all repl

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

[Chebbi Mohamed Amine]

HI Nate !

Thanks for your response. However, I have a little problem concerning the
launch of IGV application from my local galaxy tool main. In fact to run
IGV I have always to connect to my server machine where IGV is installed.
So it is embarrassing, since that other users  cannot display IGV in their
own machines when they connect to my galaxy instance.

Here above my xml file :



 java -Xmx1G -jar ~/tools/myTool/igv/igv.jar $input 
 
 
  
  
 
  


Have I to modify it or maybe proceeding bu another way 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 /
> >  
> >
> > and
> >
> > 
> > # Compress all uncompressed content.
> > SetOutputFilter DEFLATE
> > SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
> > SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
> >   
> >
> > But it dosen't fix it.
>
> Hi Amine,
>
> Did you also set use_sendfile = True in universe_wsgi.ini and restart the
> Galaxy server process?
>
> --nate
>
> >
> > I think that il is may be a problem of server byte-range accepting?
> >
> > Thanks
> > Amine
> >
> > 2012/7/4 Geert Vandeweyer 
> > Hi,
> >
> > If I remember correctly, I solved this issue by enabling the xsendfile
> module in apache and setting galaxy to use the proxy for file downloading.
> >
> > 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 encounter the following message :
> >>
> >> "HTTP and FTP access to BAM files require byte-range support"
> >>
> >> Has anyone encountred the same probleme?
> >>
> >> Thanks in advances
> >>
> >> Regards
> >> Amine
> >>
> >>
> >>
> >>
> >> ___
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >>
> >> http://lists.bx.psu.edu/
> >
> >
> > --
> >
> > Geert Vandeweyer, Ph.D.
> > Department of Medical Genetics
> > University of Antwerp
> > Prins Boudewijnlaan 43
> > 2650 Edegem
> > Belgium
> > Tel:
> > +32 (0)3 275 97 56
> >
> > E-mail:
> > geert.vandewe...@ua.ac.be
> > http://ua.ac.be/cognitivegenetics
> > http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
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[galaxy-dev] Display with IGV local

[Chebbi Mohamed Amine]

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 automatically
I guess that I have to configure bam.xml file to call "java -Xmx750m -jar
igv.jar" command ,  when cliking on D*isplay with IGV local*. ?

Thanks for help
Regards
Amine
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Re: [galaxy-dev] Byte-range support for IGV ?

[Chebbi Mohamed Amine]

HI Geert !
I did well :


XSendFile on
XSendFilePath /
 

and


# Compress all uncompressed content.
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
  

But it dosen't fix it.

I think that il is may be a problem of server byte-range accepting?

Thanks
Amine

2012/7/4 Geert Vandeweyer 

>  Hi,
>
> If I remember correctly, I solved this issue by enabling the xsendfile
> module in apache and setting galaxy to use the proxy for file downloading.
>
> 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 encounter the following message :
>
> "HTTP and FTP access to BAM files require byte-range support"
>
> Has anyone encountred the same probleme?
>
> Thanks in advances
>
> Regards
> Amine
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>   http://lists.bx.psu.edu/
>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: 
> geert.vandewe...@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>
>
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[galaxy-dev] Byte-range support for IGV ?

[Chebbi Mohamed Amine]

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?

Thanks in advances

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

[Chebbi Mohamed Amine]

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 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<http://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826466/igb_bam/Local>
> Web<http://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826466/igb_bam/Web>"
> Could someone help me .
> Thanks
> Amine
>
>
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[galaxy-dev] Display IGV link within history bam items?

[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 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
Web"
Could someone help me .
Thanks
Amine
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Re: [galaxy-dev] Port Config SMTP Server

[CHEBBI Mohamed Amine]

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 !
>> 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
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>>
>
>
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[galaxy-dev] Port Config SMTP Server

[CHEBBI Mohamed Amine]

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

[Chebbi Mohamed 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 

>
>
> On 06/19/2012 07:11 PM, Chebbi Mohamed Amine wrote:
>
>> 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 import eggs
>> ImportError: No module named galaxy
>>
>
>
> looks like you are calling the script from:
>
>  ~/galaxy_dist/scripts/cleanup_**datasets/
>
>
> try calling it with:
>
> python scripts/cleanup_datasets/**cleanup_datasets.py universe_wsgi.ini
> -d 60 -1
>
> from:  ~/galaxy_dist/
>
>
>
> Regards, Hans
>
>
>> Although I set cleanup_job = never in my Galaxy config and check the PBS
>> script like mentioned in the mailing list discussions as above , i have
>> always the same problem of galaxy module :
>>
>> GALAXY_LIB="/path/to/galaxy-**dist/lib"
>> if [ "$GALAXY_LIB" != "None" ]; then
>> if [ -n "$PYTHONPATH" ]; then
>> export PYTHONPATH="$GALAXY_LIB:$**PYTHONPATH"
>> else
>> export PYTHONPATH="$GALAXY_LIB"
>> fi
>> fi
>>
>> Could someone help me please !
>>
>> Thanks
>> Amine
>>
>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>
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[galaxy-dev] No module named galaxy !!

[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 
from galaxy import eggs
ImportError: No module named galaxy

Although I set cleanup_job = never in my Galaxy config and check the PBS
script like mentioned in the mailing list discussions as above , i have
always the same problem of galaxy module :

GALAXY_LIB="/path/to/galaxy-dist/lib"
if [ "$GALAXY_LIB" != "None" ]; then
if [ -n "$PYTHONPATH" ]; then
export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
else
export PYTHONPATH="$GALAXY_LIB"
fi
fi

Could someone help me please !

Thanks
Amine
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Re: [galaxy-dev] Proftpd Problem

[CHEBBI Mohamed Amine]

Hi Nate !
Thank-you for your response. I have finally fixed the problem. In fact I
had to add the line above in the /etc/proftpd.modules.conf :
AuthOrder mod_sql.c mod_auth_unix.c

This enables the checking of user login and password from SQL tables.
So Now I can upload data by FTP from my Galaxy 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
> > 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://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't
> connect when using Useremail .
> > the proftpd.log get this message :
> > juin 04 14:43:56 rosalind proftpd[31368] rosalind
> (193.55.24.4[193.55.24.4]): FTP session opened.
> > juin 04 14:43:56 rosalind proftpd[31368] rosalind
> (193.55.24.4[193.55.24.4]): notice: unable to use '~/' [resolved to
> '/usr/local/appli/Galaxy/$
> > juin 04 14:43:56 rosalind proftpd[31368] rosalind
> (193.55.24.4[193.55.24.4]): Preparing to chroot to directory '~/'
> > juin 04 14:43:56 rosalind proftpd[31368] rosalind
> (193.55.24.4[193.55.24.4]): chroot to '~/' failed for user '
> chebbimam...@hotmail.com': Opérat$
> > juin 04 14:43:56 rosalind proftpd[31368] rosalind
> (193.55.24.4[193.55.24.4]): error: unable to set default root directory
> > juin 04 14:43:56 rosalind proftpd[31368] rosalind
> (193.55.24.4[193.55.24.4]): FTP session closed.
> >
> > Could someone help me .
>
> Hi Amine,
>
> Could you post your proftpd.conf, with any sensitive information (e.g.
> database server address/password) removed?
>
> Thanks,
> --nate
>
> > Thanks
> > Amine
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
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[galaxy-dev] Fwd: Proftpd Problem

[CHEBBI Mohamed Amine]

-- 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://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't
connect when using Useremail .
the proftpd.log get this message :
juin 04 14:43:56 rosalind proftpd[31368] rosalind
(193.55.24.4[193.55.24.4]): FTP session opened.
juin 04 14:43:56 rosalind proftpd[31368] rosalind
(193.55.24.4[193.55.24.4]): notice: unable to use '~/' [resolved to
'/usr/local/appli/Galaxy/$
juin 04 14:43:56 rosalind proftpd[31368] rosalind
(193.55.24.4[193.55.24.4]): Preparing to chroot to directory '~/'
juin 04 14:43:56 rosalind proftpd[31368] rosalind
(193.55.24.4[193.55.24.4]): chroot to '~/' failed for user '
chebbimam...@hotmail.com': Opérat$
juin 04 14:43:56 rosalind proftpd[31368] rosalind
(193.55.24.4[193.55.24.4]): error: unable to set default root directory
juin 04 14:43:56 rosalind proftpd[31368] rosalind
(193.55.24.4[193.55.24.4]): FTP session closed.

Could someone help me .
Thanks
Amine
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[galaxy-dev] BWA Problem

[CHEBBI Mohamed Amine]

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 fault*
*
*
Could anyone help me to fix it thanks !

Regards
Amine
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[galaxy-dev] Proftpd Problem

[CHEBBI Mohamed Amine]

 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 to register 'memcache' SSL session
cache: Memcache support not enabled
Thanks,
Amine
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Re: [galaxy-dev] Running Galaxy behind apache2

[CHEBBI Mohamed Amine]

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 '/etc/apache2/sites-available/default' not
> /etc/apache2/apache2.conf.
>
> Hope it helps,
> Carlos
>
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[galaxy-dev] Fwd: Running Galaxy behind apache2

[CHEBBI Mohamed Amine]

-- 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 content has been added, yet.
Should I create a galaxy service file to enable the galaxy process
restarting?


2012/5/11 Nate Coraor 

> On May 10, 2012, at 4:23 PM, CHEBBI Mohamed Amine wrote:
>
> > Hi Galaxy team ;
> > I'am trying to put  Galaxy into a production environment behind apache2 :
> >
> > I followed the tuto in
> http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy for putting galaxy
> behind apache2 so I installed all the modules required (proxy-mod ;
> rewrite_mod etc ) and I configured the apache2.conf like above :
> >
> > RewriteEngine on
> > RewriteRule ^/static/style/(.*) /usr/local/appli/Galaxy/
> > Galaxy_dist/static/june$
> > RewriteRule ^/static/scripts/(.*)
> /usr/local/appli/Galaxy/Galaxy_dist/static/sc$
> > RewriteRule ^/static/(.*) /usr/local/appli/Galaxy/Galaxy_dist/static/$1
> [L]
> > RewriteRule ^/favicon.ico
> /usr/local/appli/Galaxy/Galaxy_dist/static/favicon.ic$
> > RewriteRule ^/robots.txt
>  /usr/local/appli/Galaxy/Galaxy_dist/static/robots.txt$
> > RewriteRule ^(.*) http://localhost:8080$1 [P]
> >
> > I modified  also the universe_wsgi.ini  galaxy file by setting: host =
> 0.0.0.0 to enable  Galaxy binding to any available network.
> >
> > After restarting apache, when t type http://xx.xxx.xx.xx:8080 it
> doesn't  establish a connection.?
>
> Hi,
>
> If you access port 8080 directly, you'd be bypassing the Apache proxy and
> going directly to Galaxy's built-in web server.  Also, if you didn't
> restart the Galaxy process after setting host = 0.0.0.0, it would still
> only be listening on localhost.
>
> What happens if you go to http:// without specifying a port number?
>
> --nate
>
> >
> > Is there a configuration more to do?
> > Thank you in advance
> > ___
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> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
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[galaxy-dev] Running Galaxy in a production environment

[CHEBBI Mohamed Amine]

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 should I do to link the Galaxy session management for an outside
application like Django

I thank you in advance.

Regards,
Amine.
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