Sorry for bumping my own question but I didn't get any replies. Has anyone succesfully installed a production Galaxy instance? I could really use some advice. Thank you, Makis From: makis4ever(a)hotmail.com To: galaxy-dev(a)lists.bx.psu.edu; galaxy-dev(a)lists.galaxyproject.org Date: Tue, 1 Dec 2015 18:03:44 +0200 Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed Hello everyone, I am trying to setup a Galaxy instance for a multi-user production environment and I tried to follow the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/ApacheProxy but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh --daemon) I got the following error in my browser:Bad Gateway The proxy server received an invalid response from an upstream server. I don't get any errors from the paster.log files so I am guessing the error is somewhere in my apache configuration although I can't see where it could be. Has anyone encountered this problem before? Kind regards, Makis P.S. My apache configuration is as follows: I added that to my apache httpd.conf file: #for galaxy #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P] RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so <Location "/galaxy"> Sethandler uwsgi-handler uWSGISocket 127.0.0.1:4001 uWSGImaxVars 512 </Location> I am also attaching my job_conf.xml and galaxy.ini file. ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

It is uwsgi that I am trying but with apache. Could you let me know what changes you made to the configuration of Galaxy? Thank you, Makis Date: Fri, 4 Dec 2015 10:01:56 +0200 Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed From: pvh(a)sanbi.ac.za To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.bx.psu.edu; galaxy-dev(a)lists.galaxyproject.org Hi Makis, I recently implemented something like this using uWSGI with a nginx frontend. Would you consider using uWSGI instead of your current approach? On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4ever(a)hotmail.com&gt; wrote: Sorry for bumping my own question but I didn't get any replies. Has anyone succesfully installed a production Galaxy instance? I could really use some advice. Thank you, Makis From: makis4ever(a)hotmail.com To: galaxy-dev(a)lists.bx.psu.edu; galaxy-dev(a)lists.galaxyproject.org Date: Tue, 1 Dec 2015 18:03:44 +0200 Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed Hello everyone, I am trying to setup a Galaxy instance for a multi-user production environment and I tried to follow the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/ApacheProxy but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh --daemon) I got the following error in my browser:Bad Gateway The proxy server received an invalid response from an upstream server. I don't get any errors from the paster.log files so I am guessing the error is somewhere in my apache configuration although I can't see where it could be. Has anyone encountered this problem before? Kind regards, Makis P.S. My apache configuration is as follows: I added that to my apache httpd.conf file: #for galaxy #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P] RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so <Location "/galaxy"> Sethandler uwsgi-handler uWSGISocket 127.0.0.1:4001 uWSGImaxVars 512 </Location> I am also attaching my job_conf.xml and galaxy.ini file. ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hello thank you for your reply. I followed the instructions on your blog together with the Galaxy tutorial and even though I changed the port to 127.0.0.1:8091 in supervisord.conf it refuses the connection: supervisorctl status http://localhost:9001 refused connection The port is the wrong one as well!!! It was 8091 the port that I used ps ax |grep uwsgi doesn't display a working uwsgi service and sudo lsof -i :4001 returns nothing. My supervisord.conf file is the following: [inet_http_server] port=127.0.0.1:8091 [supervisord] [supervisorctl] [program:galaxy_uwsgi] command = /usr/bin/uwsgi --plugin python --ini-paste /home/galaxy/galaxy/config/galaxy.ini directory = /home/galaxy/galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = PATH=/home/galaxy/galaxy_env:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHON_EGG_CACHE=/home/galaxy/galaxy/.python-eggs,PYTHONPATH=/home/galaxy/galaxy/eggs/PasteDeploy-1.5.0-py2.7.egg numprocs = 1 stopsignal = INT [program:handler] command = /home/galaxy/galaxy_env/bin/python ./scripts/paster.py serve config/galaxy.ini --server-name=handler%(process_num)s --pid-file=/home/galaxy/galaxy/handler%(process_num)s.pid --log-file=/home/galaxy/galaxy/handler%(process_num)s.log directory = /home/galaxy/galaxy process_name = handler%(process_num)s numprocs = 8 umask = 022 autostart = true autorestart = true startsecs = 15 user = galaxy environment = PYTHON_EGG_CACHE=/home/galaxy/galaxy/.python-eggs #I didn't include SGE_root as i don't have sge installed [group:galaxy] programs = handler, galaxy_uwsgi Can you help me please? What am I missing? Thank you, Makis Date: Fri, 4 Dec 2015 17:57:38 +0200 Subject: RE: [galaxy-dev] Multiple web servers and handlers Galaxy failed From: pvh(a)sanbi.ac.za To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.bx.psu.edu; galaxy-dev(a)lists.galaxyproject.org I've written up my experiences in a blog:http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/The only Galaxy side changes were the ones mentioned on the Scaling page. The Bad Gateway message means that Apache can't talk to the uWSGI so what is the state of uWSGI? Are you using supervisord? Does supervisorctl show the uWSGI process running? Does ps ax |grep uwsgi show it running? What does sudo lsof -i :4001 show is listening on port 4001? That would be the starting point of my debugging. Peter On 4 Dec 2015 10:57, "Makis Ladoukakis" <makis4ever(a)hotmail.com&gt; wrote: It is uwsgi that I am trying but with apache. Could you let me know what changes you made to the configuration of Galaxy? Thank you, Makis Date: Fri, 4 Dec 2015 10:01:56 +0200 Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed From: pvh(a)sanbi.ac.za To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.bx.psu.edu; galaxy-dev(a)lists.galaxyproject.org Hi Makis, I recently implemented something like this using uWSGI with a nginx frontend. Would you consider using uWSGI instead of your current approach? On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4ever(a)hotmail.com&gt; wrote: Sorry for bumping my own question but I didn't get any replies. Has anyone succesfully installed a production Galaxy instance? I could really use some advice. Thank you, Makis From: makis4ever(a)hotmail.com To: galaxy-dev(a)lists.bx.psu.edu; galaxy-dev(a)lists.galaxyproject.org Date: Tue, 1 Dec 2015 18:03:44 +0200 Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed Hello everyone, I am trying to setup a Galaxy instance for a multi-user production environment and I tried to follow the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/ApacheProxy but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh --daemon) I got the following error in my browser:Bad Gateway The proxy server received an invalid response from an upstream server. I don't get any errors from the paster.log files so I am guessing the error is somewhere in my apache configuration although I can't see where it could be. Has anyone encountered this problem before? Kind regards, Makis P.S. My apache configuration is as follows: I added that to my apache httpd.conf file: #for galaxy #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P] RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so <Location "/galaxy"> Sethandler uwsgi-handler uWSGISocket 127.0.0.1:4001 uWSGImaxVars 512 </Location> I am also attaching my job_conf.xml and galaxy.ini file. ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel? Thank you, Makis Ladoukakis From: makis4ever(a)hotmail.com To: galaxy-dev(a)lists.bx.psu.edu Date: Wed, 16 Dec 2015 13:41:19 +0200 Subject: [galaxy-dev] Collapse tool panel and history panel Hello, Does anyone know how to start my Galaxy instance with the history panel and tool panel collapsed by default? I used to do it by editing the galaxy/templates/base/base_panels.mako script and adding lp.do_toggle(); and rp.do_toggle(); inside the if sections of %if self.has_left_panel: and %if self.has_right_panel: respectively but with my new installed instance this doesn't seem to work anymore. Any ideas anyone? Thank you, Makis Ladoukakis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hello Dannon, Sorry for asking but can you help me out a little bit with that? I searched in my galaxy directory in order to add those two lines you mention in the link but there is no galaxy/scripts/apps/analysis.js file and neither any file containing the string 'analysisPage.right.historyView'. Any advice? Thank you, Makis Date: Mon, 28 Dec 2015 14:30:02 -0500 Subject: Re: [galaxy-dev] Collapse tool panel and history panel From: dannon.baker(a)gmail.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.bx.psu.edu Hi Makis, We've restructured much of the client code fairly recently. Something like this should work for you now: https://gist.github.com/dannon/bd470d9c70019b07cb8b Sorry for the slow response! -Dannon On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis <makis4ever(a)hotmail.com&gt; wrote: Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel? Thank you, Makis Ladoukakis From: makis4ever(a)hotmail.com To: galaxy-dev(a)lists.bx.psu.edu Date: Wed, 16 Dec 2015 13:41:19 +0200 Subject: [galaxy-dev] Collapse tool panel and history panel Hello, Does anyone know how to start my Galaxy instance with the history panel and tool panel collapsed by default? I used to do it by editing the galaxy/templates/base/base_panels.mako script and adding lp.do_toggle(); and rp.do_toggle(); inside the if sections of %if self.has_left_panel: and %if self.has_right_panel: respectively but with my new installed instance this doesn't seem to work anymore. Any ideas anyone? Thank you, Makis Ladoukakis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

The git log ..origin/master command produced no output so I guess I have the latest release (15.10.1 maybe?). The git pull command confirmed that. Should I use a release from the dev branch? Kind regards, Makis Date: Fri, 19 Feb 2016 08:39:35 -0500 Subject: Re: [galaxy-dev] Collapse tool panel and history panel From: dannon.baker(a)gmail.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.bx.psu.edu Sure, I can help. Which version of Galaxy are you currently running? I didn't check the history very well and the fix I suggested will work for the forthcoming 16.01 release (or current dev branch), but not 15.10. On Fri, Feb 19, 2016 at 8:32 AM, Makis Ladoukakis <makis4ever(a)hotmail.com&gt; wrote: Hello Dannon, Sorry for asking but can you help me out a little bit with that? I searched in my galaxy directory in order to add those two lines you mention in the link but there is no galaxy/scripts/apps/analysis.js file and neither any file containing the string 'analysisPage.right.historyView'. Any advice? Thank you, Makis Date: Mon, 28 Dec 2015 14:30:02 -0500 Subject: Re: [galaxy-dev] Collapse tool panel and history panel From: dannon.baker(a)gmail.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.bx.psu.edu Hi Makis, We've restructured much of the client code fairly recently. Something like this should work for you now: https://gist.github.com/dannon/bd470d9c70019b07cb8b Sorry for the slow response! -Dannon On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis <makis4ever(a)hotmail.com&gt; wrote: Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel? Thank you, Makis Ladoukakis From: makis4ever(a)hotmail.com To: galaxy-dev(a)lists.bx.psu.edu Date: Wed, 16 Dec 2015 13:41:19 +0200 Subject: [galaxy-dev] Collapse tool panel and history panel Hello, Does anyone know how to start my Galaxy instance with the history panel and tool panel collapsed by default? I used to do it by editing the galaxy/templates/base/base_panels.mako script and adding lp.do_toggle(); and rp.do_toggle(); inside the if sections of %if self.has_left_panel: and %if self.has_right_panel: respectively but with my new installed instance this doesn't seem to work anymore. Any ideas anyone? Thank you, Makis Ladoukakis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hi Makis, if you change the javascript in client/ ... you need to run grunt. The instructions are in https://github.com/galaxyproject/galaxy/blob/dev/client/README.md. Cheers, Marius On 25 February 2016 at 10:57, Makis Ladoukakis <makis4ever(a)hotmail.com&gt; wrote:

Hi Makis, as a small pointer, please have a look at the ansible playrole we provide: https://github.com/galaxyproject/ansible-galaxy-extras or the Galaxy Docker Image: https://github.com/bgruening/docker-galaxy-stable all steps are described here and can be reused. Cheers, Bjoern Am 04.12.2015 um 08:39 schrieb Makis Ladoukakis: