[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 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/
Re: [galaxy-dev] Using an unique database for tow differents versions of Galaxy
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 dannonba...@me.com 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 boseprom...@gmail.com 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 ja...@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 2012/9/21 James Taylor ja...@jamestaylor.org 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 chebbimam...@gmail.com 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/ ___ 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/
[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/TLEngine. Please check that the keyword arguments are appropriate for this combination of components. 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/
Re: [galaxy-dev] Galaxy crach while visualization
Ok Jeremy ; So I will test the latest release. Thanks Amine 2012/7/25 Jeremy Goecks jeremy.goe...@emory.edu 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 chebbimam...@gmail.com 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 jeremy.goe...@emory.edu 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=chr19low=1449105high=1449853mode=Packresolution=1.8693312836279785dataset_id=7350596ac236c69dhda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Packresolution=2.3339731285988483dataset_id=2a8867ca0da68ac1hda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Autoresolution=2.3339731285988483dataset_id=18644201db609b11hda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Packresolution=2.3339731285988483dataset_id=7350596ac236c69dhda_ldda=hdafilter_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 - type 'exceptions.IOError': could not open index `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat` 2012/7/19 Jeremy Goecks jeremy.goe...@emory.edu 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 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 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 jeremy.goe...@emory.edu 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
[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 ___ 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/
Re: [galaxy-dev] Galaxy crach while visualization
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 jeremy.goe...@emory.edu 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=chr19low=1449105high=1449853mode=Packresolution=1.8693312836279785dataset_id=7350596ac236c69dhda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Packresolution=2.3339731285988483dataset_id=2a8867ca0da68ac1hda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Autoresolution=2.3339731285988483dataset_id=18644201db609b11hda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Packresolution=2.3339731285988483dataset_id=7350596ac236c69dhda_ldda=hdafilter_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 - type 'exceptions.IOError': could not open index `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat` 2012/7/19 Jeremy Goecks jeremy.goe...@emory.edu 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 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 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 jeremy.goe...@emory.edu 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=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=f4b17be90d9b3c9dhda_ldda=hdafilter_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
Re: [galaxy-dev] Galaxy crach while visualization
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=chr19low=1449105high=1449853mode=Packresolution=1.8693312836279785dataset_id=7350596ac236c69dhda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Packresolution=2.3339731285988483dataset_id=2a8867ca0da68ac1hda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Autoresolution=2.3339731285988483dataset_id=18644201db609b11hda_ldda=hdafilter_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=chr19low=1457332high=1458266mode=Packresolution=2.3339731285988483dataset_id=7350596ac236c69dhda_ldda=hdafilter_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 - type 'exceptions.IOError': could not open index `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat` 2012/7/19 Jeremy Goecks jeremy.goe...@emory.edu 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 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 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 jeremy.goe...@emory.edu 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=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=f4b17be90d9b3c9dhda_ldda=hdafilter_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=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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
[galaxy-dev] Fwd: Galaxy crach while visualization
-- 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 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 jeremy.goe...@emory.edu 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=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=f4b17be90d9b3c9dhda_ldda=hdafilter_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=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1180427high=1181609mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_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=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_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=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_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=chr19low=814128high=815310mode=Autoresolution=2.954022988505747dataset_id=7710e7c5028b7c3bhda_ldda=hdafilter_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
[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/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=f4b17be90d9b3c9dhda_ldda=hdafilter_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=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_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=chr19low=1180427high=1181609mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_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=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_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=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_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=chr19low=814128high=815310mode=Autoresolution=2.954022988505747dataset_id=7710e7c5028b7c3bhda_ldda=hdafilter_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 replies on the list by using reply all in your mail client. To manage your subscriptions to this and other
[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 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 ___ 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/
[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? 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/
[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 (display file=igv/bam.xml /). However the Links dose not appear in bam history items. I see only display in IGB Localhttp://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826466/igb_bam/Local Webhttp://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826466/igb_bam/Web Could someone help me . 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/
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 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 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 Localhttp://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826466/igb_bam/Local Webhttp://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826466/igb_bam/Web Could someone help me . 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/
Re: [galaxy-dev] Port Config SMTP Server
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. 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/ ___ 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/
[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 ___ 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/
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 h...@fmi.ch 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 module 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/ ___ 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/
[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 module 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 ___ 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/
Re: [galaxy-dev] Proftpd Problem
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 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 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/ ___ 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/
[galaxy-dev] Fwd: Proftpd Problem
-- 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 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 ___ 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/
[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 fault* * * Could anyone help me to fix it thanks ! 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/
[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 to register 'memcache' SSL session cache: Memcache support not enabled 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/
[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 should I do to link the Galaxy session management for an outside application like Django I thank you in advance. 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/
