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@sanbi.ac.za To: makis4ever@hotmail.com CC: galaxy-dev@lists.bx.psu.edu; galaxy-dev@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@hotmail.com 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@hotmail.com To: galaxy-dev@lists.bx.psu.edu; galaxy-dev@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.

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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@sanbi.ac.za To: makis4ever@hotmail.com CC: galaxy-dev@lists.bx.psu.edu; galaxy-dev@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@hotmail.com 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@sanbi.ac.za To: makis4ever@hotmail.com CC: galaxy-dev@lists.bx.psu.edu; galaxy-dev@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@hotmail.com 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@hotmail.com To: galaxy-dev@lists.bx.psu.edu; galaxy-dev@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/

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___________________________________________________________

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Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel?

Thank you, Makis Ladoukakis

From: makis4ever@hotmail.com To: galaxy-dev@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/

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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@gmail.com To: makis4ever@hotmail.com CC: galaxy-dev@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@hotmail.com wrote:

Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel?

Thank you, Makis Ladoukakis

From: makis4ever@hotmail.com To: galaxy-dev@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:

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To search Galaxy mailing lists use the unified search at:

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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@gmail.com To: makis4ever@hotmail.com CC: galaxy-dev@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@hotmail.com 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@gmail.com To: makis4ever@hotmail.com CC: galaxy-dev@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@hotmail.com wrote:

Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel?

Thank you, Makis Ladoukakis

From: makis4ever@hotmail.com To: galaxy-dev@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:

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To search Galaxy mailing lists use the unified search at:

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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@hotmail.com wrote:

Just an update/bump of the issue. With the new 16.01 version I made the changes in the /client/galaxy/scripts/apps/analysis.js b/client/galaxy/scripts/apps/analysis.js file but the none of the panels were collapsed even when i restarted my Galaxy instance.

I don't really get the mechanics behind it. Seems like any changes i do either in the js files or the mako scripts never take effect in the actual instance. I even tried to delete everything in there leaving just a blank file to test my theory and after restart the Galaxy instance initializes with no errors at all.

Any ideas? Makis

---

From: makis4ever@hotmail.com To: dannon.baker@gmail.com Date: Mon, 22 Feb 2016 13:47:59 +0200 CC: galaxy-dev@lists.bx.psu.edu

Subject: Re: [galaxy-dev] Collapse tool panel and history panel

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@gmail.com To: makis4ever@hotmail.com CC: galaxy-dev@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@hotmail.com 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@gmail.com To: makis4ever@hotmail.com CC: galaxy-dev@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@hotmail.com wrote:

Shamelessly bumping my own question... Does anyone have any ideas about collapsing the history and tool panel?

Thank you, Makis Ladoukakis

---

From: makis4ever@hotmail.com To: galaxy-dev@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/

---

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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:

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@hotmail.com To: galaxy-dev@lists.bx.psu.edu; galaxy-dev@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.

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