Re: [galaxy-dev] How must I configure Apache ?
Yes a follow this wiki but it doesn't work. I've tried to post too in
apache forum because may be it's simply a problem with apache.
thank you for your help.
Julie
2012/5/24 Carlos Borroto
> Glad it helped.
>
> About configuring Galaxy to use port 8080, other than what you are
> already doing, checking for another process already using the port, I
> wouldn't know what to recommend.
>
> About the balancing configuration, I haven't done it, so I don't have
> much to help with that. I do think it should go in the virtual host
> configuration file(default) and I don't think it should matter if you
> put it before or after the rewrite rules.
>
> Are you following the instructions in?:
>
> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
>
> Regards,
> Carlos
>
> On Mon, May 21, 2012 at 4:17 AM, julie dubois wrote:
> > Hi,
> > Thanks for your answer.
> > Effectively it's not necessary on integrating Galaxy with a third party
> > authentication system.
> > I've integrated my configuration to the file "default" and it's work !
> >
> > Just one remark. I've configured the file ports.conf with the line :
> > "Listen 8080", and it didn't work!
> > In fact, the shell says me that the galaxy port was already in use while
> the
> > command lsof -ti : 8080 showed no result.
> > And when I delete the line "listen 8080" of my file ports.conf, Galaxy
> work!
> > Is it normal ?
> >
> > Finally, if I want tu use the proxy balancer lines like this (it is in
> the
> > hope to increase performances):
> >
> > Balancer member...
> > ...
> >
> >
> > must I add in default file (and before or after the rewrite rules?) or
> in an
> > other file ?
> >
> > Thank you in advance.
> > Julie
> >
> > 2012/5/18 Carlos Borroto
> >>
> >> Hi Julie,
> >>
> >> Could you answer a couple of questions?
> >>
> >> First, are you interested on integrating Galaxy with a third party
> >> authentication system?
> >>
> >> Second, do you expect heavy usage(I would say hundreds of concurrent
> >> users) where you would need several Galaxy servers with the work load
> >> balanced amount them?. Note even if you only have one Galaxy server,
> >> you will still have several Apache processes running and you will be
> >> able to serve multiple concurrent users without issue. Well at least
> >> from the web server side of things, if you expect even a moderate
> >> usage you should use a database back-end like PostgreSQL or MySQL.
> >>
> >> If the answer to these questions is no, all you need in a
> >> Debian/Ubuntu system is to place this in
> >> '/etc/apache2/sites-available/default' file between the
> >> tags:
> >> RewriteEngine on
> >> RewriteRule ^/static/style/(.*)
> >> /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> >> RewriteRule ^/static/scripts/(.*)
> >> /home/nate/galaxy-dist/static/scripts/packed/$1 [L]
> >> RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> >> RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
> >> RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> >> RewriteRule ^(.*) http://localhost:8080$1 [P]
> >>
> >> Even if the answer if yes to both questions, I would start with the
> >> simpler setup first, get it working and then grow from there.
> >>
> >> Hope it helps,
> >> Carlos
> >>
> >> On Fri, May 18, 2012 at 6:59 AM, julie dubois
> wrote:
> >> > Hi,
> >> > First, Sorry but, I'm a newbie with Apache and my questions will
> >> > certainly
> >> > appear stupid.
> >> >
> >> > To configure apache2, I've followed this wiki :
> >> > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
> >> > And I write these instructions :
> >> >
> >> > http://localhost:8080>
> >> > Order deny,allow
> >> > Allow from all
> >> >
> >> > RewriteEngine on
> >> >
> >> > # Define the authentication method
> >> > AuthType Basic
> >> > AuthName Galaxy
> >> > AuthUserFile /home/nate/htpasswd
> >> > Require valid-user
> >> > # Take the $REMOTE_USER environment variable and set it as a
> header
> >> > in
> >> > the proxy request.
> >> > RewriteCond %{IS_SUBREQ} ^false$
> >> > RewriteCond %{LA-U:REMOTE_USER} (.+)
> >> > RewriteRule . - [E=RU:%1]
> >> > RequestHeader set REMOTE_USER %{RU}e
> >> >
> >> > RewriteRule ^/static/style/(.*)
> >> > /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> >> > RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> >> > RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico
> [L]
> >> > RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> >> > RewriteRule ^(.*) http://localhost:8080$1 [P]
> >> >
> >> >
> >> >
> >> >
> >> > But several problems appeared when I launched my Galaxy.
> >> >
> >> >
> >> > First, must this instructions block be in the file apache2.conf or in
> >> > the
> >> > file default of sites-available directory ?
> >> > If it must be in the file default, is it between the
> tags
> >> > or
>
Re: [galaxy-dev] How must I configure Apache ?
Glad it helped.
About configuring Galaxy to use port 8080, other than what you are
already doing, checking for another process already using the port, I
wouldn't know what to recommend.
About the balancing configuration, I haven't done it, so I don't have
much to help with that. I do think it should go in the virtual host
configuration file(default) and I don't think it should matter if you
put it before or after the rewrite rules.
Are you following the instructions in?:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
Regards,
Carlos
On Mon, May 21, 2012 at 4:17 AM, julie dubois wrote:
> Hi,
> Thanks for your answer.
> Effectively it's not necessary on integrating Galaxy with a third party
> authentication system.
> I've integrated my configuration to the file "default" and it's work !
>
> Just one remark. I've configured the file ports.conf with the line :
> "Listen 8080", and it didn't work!
> In fact, the shell says me that the galaxy port was already in use while the
> command lsof -ti : 8080 showed no result.
> And when I delete the line "listen 8080" of my file ports.conf, Galaxy work!
> Is it normal ?
>
> Finally, if I want tu use the proxy balancer lines like this (it is in the
> hope to increase performances):
>
> Balancer member...
> ...
>
>
> must I add in default file (and before or after the rewrite rules?) or in an
> other file ?
>
> Thank you in advance.
> Julie
>
> 2012/5/18 Carlos Borroto
>>
>> Hi Julie,
>>
>> Could you answer a couple of questions?
>>
>> First, are you interested on integrating Galaxy with a third party
>> authentication system?
>>
>> Second, do you expect heavy usage(I would say hundreds of concurrent
>> users) where you would need several Galaxy servers with the work load
>> balanced amount them?. Note even if you only have one Galaxy server,
>> you will still have several Apache processes running and you will be
>> able to serve multiple concurrent users without issue. Well at least
>> from the web server side of things, if you expect even a moderate
>> usage you should use a database back-end like PostgreSQL or MySQL.
>>
>> If the answer to these questions is no, all you need in a
>> Debian/Ubuntu system is to place this in
>> '/etc/apache2/sites-available/default' file between the
>> tags:
>> RewriteEngine on
>> RewriteRule ^/static/style/(.*)
>> /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
>> RewriteRule ^/static/scripts/(.*)
>> /home/nate/galaxy-dist/static/scripts/packed/$1 [L]
>> RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
>> RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
>> RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
>> RewriteRule ^(.*) http://localhost:8080$1 [P]
>>
>> Even if the answer if yes to both questions, I would start with the
>> simpler setup first, get it working and then grow from there.
>>
>> Hope it helps,
>> Carlos
>>
>> On Fri, May 18, 2012 at 6:59 AM, julie dubois wrote:
>> > Hi,
>> > First, Sorry but, I'm a newbie with Apache and my questions will
>> > certainly
>> > appear stupid.
>> >
>> > To configure apache2, I've followed this wiki :
>> > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
>> > And I write these instructions :
>> >
>> > http://localhost:8080>
>> > Order deny,allow
>> > Allow from all
>> >
>> > RewriteEngine on
>> >
>> > # Define the authentication method
>> > AuthType Basic
>> > AuthName Galaxy
>> > AuthUserFile /home/nate/htpasswd
>> > Require valid-user
>> > # Take the $REMOTE_USER environment variable and set it as a header
>> > in
>> > the proxy request.
>> > RewriteCond %{IS_SUBREQ} ^false$
>> > RewriteCond %{LA-U:REMOTE_USER} (.+)
>> > RewriteRule . - [E=RU:%1]
>> > RequestHeader set REMOTE_USER %{RU}e
>> >
>> > RewriteRule ^/static/style/(.*)
>> > /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
>> > RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
>> > RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
>> > RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
>> > RewriteRule ^(.*) http://localhost:8080$1 [P]
>> >
>> >
>> >
>> >
>> > But several problems appeared when I launched my Galaxy.
>> >
>> >
>> > First, must this instructions block be in the file apache2.conf or in
>> > the
>> > file default of sites-available directory ?
>> > If it must be in the file default, is it between the tags
>> > or
>> > out of these tags ?
>> >
>> > Second, I've created an htpaswd file in my home directory, but when I
>> > launch
>> > galaxy, it doesn't request me a login and password but it says me that
>> > Galaxy requires an user authentification and it must be an error in my
>> > apache configuration.
>> > Is it a problem with the instructions or with their place in
>> > configuration
>> > file ?
>> >
>> > Third the line appears two times in your instructions but
>
Re: [galaxy-dev] How must I configure Apache ?
Hi,
Thanks for your answer.
Effectively it's not necessary on integrating Galaxy with a third party
authentication system.
I've integrated my configuration to the file "default" and it's work !
Just one remark. I've configured the file ports.conf with the line :
"Listen 8080", and it didn't work!
In fact, the shell says me that the galaxy port was already in use while
the command lsof -ti : 8080 showed no result.
And when I delete the line "listen 8080" of my file ports.conf, Galaxy work!
Is it normal ?
Finally, if I want tu use the proxy balancer lines like this (it is in the
hope to increase performances):
Balancer member...
...
must I add in default file (and before or after the rewrite rules?) or in
an other file ?
Thank you in advance.
Julie
2012/5/18 Carlos Borroto
> Hi Julie,
>
> Could you answer a couple of questions?
>
> First, are you interested on integrating Galaxy with a third party
> authentication system?
>
> Second, do you expect heavy usage(I would say hundreds of concurrent
> users) where you would need several Galaxy servers with the work load
> balanced amount them?. Note even if you only have one Galaxy server,
> you will still have several Apache processes running and you will be
> able to serve multiple concurrent users without issue. Well at least
> from the web server side of things, if you expect even a moderate
> usage you should use a database back-end like PostgreSQL or MySQL.
>
> If the answer to these questions is no, all you need in a
> Debian/Ubuntu system is to place this in
> '/etc/apache2/sites-available/default' file between the
> tags:
> RewriteEngine on
> RewriteRule ^/static/style/(.*)
> /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/static/scripts/(.*)
> /home/nate/galaxy-dist/static/scripts/packed/$1 [L]
> RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
> RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
> Even if the answer if yes to both questions, I would start with the
> simpler setup first, get it working and then grow from there.
>
> Hope it helps,
> Carlos
>
> On Fri, May 18, 2012 at 6:59 AM, julie dubois wrote:
> > Hi,
> > First, Sorry but, I'm a newbie with Apache and my questions will
> certainly
> > appear stupid.
> >
> > To configure apache2, I've followed this wiki :
> > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
> > And I write these instructions :
> >
> > http://localhost:8080>
> > Order deny,allow
> > Allow from all
> >
> > RewriteEngine on
> >
> > # Define the authentication method
> > AuthType Basic
> > AuthName Galaxy
> > AuthUserFile /home/nate/htpasswd
> > Require valid-user
> > # Take the $REMOTE_USER environment variable and set it as a header
> in
> > the proxy request.
> > RewriteCond %{IS_SUBREQ} ^false$
> > RewriteCond %{LA-U:REMOTE_USER} (.+)
> > RewriteRule . - [E=RU:%1]
> > RequestHeader set REMOTE_USER %{RU}e
> >
> > RewriteRule ^/static/style/(.*)
> > /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> > RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> > RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
> > RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> > RewriteRule ^(.*) http://localhost:8080$1 [P]
> >
> >
> >
> >
> > But several problems appeared when I launched my Galaxy.
> >
> >
> > First, must this instructions block be in the file apache2.conf or in the
> > file default of sites-available directory ?
> > If it must be in the file default, is it between the tags
> or
> > out of these tags ?
> >
> > Second, I've created an htpaswd file in my home directory, but when I
> launch
> > galaxy, it doesn't request me a login and password but it says me that
> > Galaxy requires an user authentification and it must be an error in my
> > apache configuration.
> > Is it a problem with the instructions or with their place in
> configuration
> > file ?
> >
> > Third the line appears two times in your instructions but
> it's
> > wrong for apache. I've deleted the first but I'm note sure that Rewrite
> > instructions must be in the block.
> >
> > And finally, I want to work with severals web processes and I want to add
> > this configuration lines :
> >
> >
> > ...
> >
> >
> > Must I add to previous lines and where ? or Must I replace certain lines
> of
> > previous block and if yes : which lines ?
> >
> > Thank you very much.
> >
> > Julie
> >
> > ___
> > 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
Re: [galaxy-dev] How must I configure Apache ?
Hi Julie,
Could you answer a couple of questions?
First, are you interested on integrating Galaxy with a third party
authentication system?
Second, do you expect heavy usage(I would say hundreds of concurrent
users) where you would need several Galaxy servers with the work load
balanced amount them?. Note even if you only have one Galaxy server,
you will still have several Apache processes running and you will be
able to serve multiple concurrent users without issue. Well at least
from the web server side of things, if you expect even a moderate
usage you should use a database back-end like PostgreSQL or MySQL.
If the answer to these questions is no, all you need in a
Debian/Ubuntu system is to place this in
'/etc/apache2/sites-available/default' file between the
tags:
RewriteEngine on
RewriteRule ^/static/style/(.*)
/home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/home/nate/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
Even if the answer if yes to both questions, I would start with the
simpler setup first, get it working and then grow from there.
Hope it helps,
Carlos
On Fri, May 18, 2012 at 6:59 AM, julie dubois wrote:
> Hi,
> First, Sorry but, I'm a newbie with Apache and my questions will certainly
> appear stupid.
>
> To configure apache2, I've followed this wiki :
> http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
> And I write these instructions :
>
> http://localhost:8080>
> Order deny,allow
> Allow from all
>
> RewriteEngine on
>
> # Define the authentication method
> AuthType Basic
> AuthName Galaxy
> AuthUserFile /home/nate/htpasswd
> Require valid-user
> # Take the $REMOTE_USER environment variable and set it as a header in
> the proxy request.
> RewriteCond %{IS_SUBREQ} ^false$
> RewriteCond %{LA-U:REMOTE_USER} (.+)
> RewriteRule . - [E=RU:%1]
> RequestHeader set REMOTE_USER %{RU}e
>
> RewriteRule ^/static/style/(.*)
> /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
> RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
>
>
>
> But several problems appeared when I launched my Galaxy.
>
>
> First, must this instructions block be in the file apache2.conf or in the
> file default of sites-available directory ?
> If it must be in the file default, is it between the tags or
> out of these tags ?
>
> Second, I've created an htpaswd file in my home directory, but when I launch
> galaxy, it doesn't request me a login and password but it says me that
> Galaxy requires an user authentification and it must be an error in my
> apache configuration.
> Is it a problem with the instructions or with their place in configuration
> file ?
>
> Third the line appears two times in your instructions but it's
> wrong for apache. I've deleted the first but I'm note sure that Rewrite
> instructions must be in the block.
>
> And finally, I want to work with severals web processes and I want to add
> this configuration lines :
>
>
> ...
>
>
> Must I add to previous lines and where ? or Must I replace certain lines of
> previous block and if yes : which lines ?
>
> Thank you very much.
>
> Julie
>
> ___
> 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] How must I configure Apache ?
Hi,
First, Sorry but, I'm a newbie with Apache and my questions will certainly
appear stupid.
To configure apache2, I've followed this wiki :
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
And I write these instructions :
http://localhost:8080> Order deny,allow Allow from all
RewriteEngine on # Define the
authentication method AuthType Basic AuthName Galaxy
AuthUserFile /home/nate/htpasswd Require valid-user # Take the
$REMOTE_USER environment variable and set it as a header in the proxy
request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond
%{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e RewriteRule
^/static/style/(.*)
/home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
^/static/(.*) /home/nate/galaxy-dist/static/$1 [L] RewriteRule
^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
But several problems appeared when I launched my Galaxy.
First, must this instructions block be in the file apache2.conf or in the
file default of sites-available directory ?
If it must be in the file default, is it between the tags or
out of these tags ?
Second, I've created an htpaswd file in my home directory, but when I
launch galaxy, it doesn't request me a login and password but it says me
that Galaxy requires an user authentification and it must be an error in my
apache configuration.
Is it a problem with the instructions or with their place in configuration
file ?
Third the line appears two times in your instructions but it's
wrong for apache. I've deleted the first but I'm note sure that Rewrite
instructions must be in the block.
And finally, I want to work with severals web processes and I want to add
this configuration lines :
...
Must I add to previous lines and where ? or Must I replace certain lines of
previous block and if yes : which lines ?
Thank you very much.
Julie
___
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/
