Apache configuration problem
Hi all, I am trying to set up httpd to serve galaxy from the root url and to serve static content as described on http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy. I will not serve Galaxy under a subdirectory. I have added to /etc/httpd/conf.d/ a file galaxy.conf with contents (CentOS system): RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] Everything works after firing up httpd! :-) But when adding following rewrite rules: RewriteRule ^/static/style/(.*)/home/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*)/home/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*)/home/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/favicon.ico/home/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/robots.txt/home/galaxy/galaxy_dist/static/robots.txt [L] I get a page which is totally scrambled. At first sight, seems to be file permission problems. The apache log file (/var/log/httpd/error_log) shows (last two lines, but the lines before these are similar): *[Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/root/tool_menu [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/history* Has anybody a clue on what I should do? I thought I will try these steps: - I changed the group owner of several of the directories recursively to the apache group - I have set the SELinux permissions with *chcon -R -h -t httpd_sys_content_t static* but no joy! :-( Thanks for any hint. Joachim
Hi Joachim, I'm not sure what's wrong with your setup, but for what it's worth I could not get the provided instructions to work properly either, when I combined the proxy with a step to authenticate against our University's single-sign service (CAS). Not sure if you're going to do authentication as well, but here are the Apache proxy directives I got to work... ProxyVia On ProxyPassInterpolateEnv On <Proxy *> Order deny,allow Allow from all </Proxy> ProxyPass / http://localhost:8080/ Cheers, Paul Joachim Jacob wrote:
Hi all,
I am trying to set up httpd to serve galaxy from the root url and to serve static content as described on http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy. I will not serve Galaxy under a subdirectory.
I have added to /etc/httpd/conf.d/ a file galaxy.conf with contents (CentOS system): RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P]
Everything works after firing up httpd! :-)
But when adding following rewrite rules: RewriteRule ^/static/style/(.*) /home/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /home/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/favicon.ico /home/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/galaxy/galaxy_dist/static/robots.txt [L]
I get a page which is totally scrambled. At first sight, seems to be file permission problems. The apache log file (/var/log/httpd/error_log) shows (last two lines, but the lines before these are similar):
*[Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/root/tool_menu [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/history*
Has anybody a clue on what I should do? I thought I will try these steps: - I changed the group owner of several of the directories recursively to the apache group - I have set the SELinux permissions with *chcon -R -h -t httpd_sys_content_t static*
but no joy! :-(
Thanks for any hint.
Joachim
------------------------------------------------------------------------
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-- ______________ Paul Gordon Bioinformatics Support Specialist Alberta Children's Hospital Research Institute http://www.ucalgary.ca/~gordonp
Hi, I am having the same problem. I am running Galaxy an Mac.OS tiger 10.6. I was wondering if there was a solution suggested. Thanks. -Sohail From: Paul Gordon <gordonp@ucalgary.ca> To: joachim.jacob@vib.be Cc: galaxy-dev@lists.bx.psu.edu Date: 08/02/2011 03:37 PM Subject: Re: [galaxy-dev] Apache configuration problem Sent by: galaxy-dev-bounces@lists.bx.psu.edu Hi Joachim, I'm not sure what's wrong with your setup, but for what it's worth I could not get the provided instructions to work properly either, when I combined the proxy with a step to authenticate against our University's single-sign service (CAS). Not sure if you're going to do authentication as well, but here are the Apache proxy directives I got to work... ProxyVia On ProxyPassInterpolateEnv On <Proxy *> Order deny,allow Allow from all </Proxy> ProxyPass / http://localhost:8080/ Cheers, Paul Joachim Jacob wrote: Hi all, I am trying to set up httpd to serve galaxy from the root url and to serve static content as described on http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy. I will not serve Galaxy under a subdirectory. I have added to /etc/httpd/conf.d/ a file galaxy.conf with contents (CentOS system): RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] Everything works after firing up httpd! :-) But when adding following rewrite rules: RewriteRule ^/static/style/(.*) /home/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /home/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/favicon.ico /home/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/galaxy/galaxy_dist/static/robots.txt [L] I get a page which is totally scrambled. At first sight, seems to be file permission problems. The apache log file (/var/log/httpd/error_log) shows (last two lines, but the lines before these are similar): [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/root/tool_menu [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: http://x.x.x.x/history Has anybody a clue on what I should do? I thought I will try these steps: - I changed the group owner of several of the directories recursively to the apache group - I have set the SELinux permissions with chcon -R -h -t httpd_sys_content_t static but no joy! :-( Thanks for any hint. Joachim ___________________________________________________________ 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/ -- ______________ Paul Gordon Bioinformatics Support Specialist Alberta Children's Hospital Research Institute http://www.ucalgary.ca/~gordonp ___________________________________________________________ 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/
Hi, The solution to my problem was very simple: I copy/pasted the code from the website, but forgot to change the name of the galaxy directory from *galaxy_dist* to *galaxy-dist*. Since this directory did not exists, he could not find the contents. Out of honesty I must say I changed the group permissions to Apache and also set the SELinux permissions with chcon. Good luck! Cheers, Joachim On 08/04/11 16:59, sohkhan@notes.cc.sunysb.edu wrote:
Hi,
I am having the same problem. I am running Galaxy an Mac.OS tiger 10.6. I was wondering if there was a solution suggested. Thanks.
-Sohail
From: Paul Gordon <gordonp@ucalgary.ca> To: joachim.jacob@vib.be Cc: galaxy-dev@lists.bx.psu.edu Date: 08/02/2011 03:37 PM Subject: Re: [galaxy-dev] Apache configuration problem Sent by: galaxy-dev-bounces@lists.bx.psu.edu ------------------------------------------------------------------------
Hi Joachim,
I'm not sure what's wrong with your setup, but for what it's worth I could not get the provided instructions to work properly either, when I combined the proxy with a step to authenticate against our University's single-sign service (CAS). Not sure if you're going to do authentication as well, but here are the Apache proxy directives I got to work...
ProxyVia On ProxyPassInterpolateEnv On <Proxy *> Order deny,allow Allow from all </Proxy> ProxyPass / _http://localhost:8080/_
Cheers,
Paul
Joachim Jacob wrote: Hi all,
I am trying to set up httpd to serve galaxy from the root url and to serve static content as described on _http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy_. I will not serve Galaxy under a subdirectory.
I have added to /etc/httpd/conf.d/ a file galaxy.conf with contents (CentOS system): *RewriteEngine* *on* *RewriteRule* ^(.*) _http://localhost:8080$1_ <http://localhost:8080$1/>[P]
Everything works after firing up httpd! :-)
But when adding following rewrite rules: *RewriteRule* ^/static/style/(.*) //home/galaxy/galaxy_dist/static/june_2007_style/blue//$1 [L] *RewriteRule* ^/static/scripts/(.*) //home/galaxy/galaxy_dist/static/scripts/packed//$1 [L] *RewriteRule* ^/static/(.*) //home/galaxy/galaxy_dist/static//$1 [L] *RewriteRule* ^/favicon.ico //home/galaxy/galaxy_dist/static/favicon.ico/[L] *RewriteRule* ^/robots.txt //home/galaxy/galaxy_dist/static/robots.txt/[L]
I get a page which is totally scrambled. At first sight, seems to be file permission problems. The apache log file (/var/log/httpd/error_log) shows (last two lines, but the lines before these are similar): * [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: **_http://x.x.x.x/root/tool_menu_** [Tue Aug 02 15:26:03 2011] [error] [client x.x.x.x] File does not exist: /home/galaxy/galaxy_dist, referer: **_http://x.x.x.x/history_*
Has anybody a clue on what I should do? I thought I will try these steps: - I changed the group owner of several of the directories recursively to the apache group - I have set the SELinux permissions with *chcon -R -h -t httpd_sys_content_t static*
but no joy! :-(
Thanks for any hint.
Joachim
------------------------------------------------------------------------
___________________________________________________________ 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:
-- ______________ Paul Gordon Bioinformatics Support Specialist Alberta Children's Hospital Research Institute _http://www.ucalgary.ca/~gordonp_ <http://www.ucalgary.ca/%7Egordonp> ___________________________________________________________ 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:
Hi, I have the production Galaxy setup and running on Mac OS Leopard 10.6, with postgres and apache. However, I am unable to run it as daemon. I don't get an error, the browser just hangs there. Thanks for any advice. -Sohail
sohkhan@notes.cc.sunysb.edu wrote:
Hi, I have the production Galaxy setup and running on Mac OS Leopard 10.6, with postgres and apache. However, I am unable to run it as daemon. I don't get an error, the browser just hangs there. Thanks for any advice.
Hi Sohail, How are you starting the daemon? Have you checked the log file to see if there are any errors? If the Galaxy process has started correctly, have you checked to see if the system firewall is enabled? --nate
-Sohail
___________________________________________________________ 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:
Hi, I have the admin user set in universe_wsgi.ini file, but I am unable to login to Galaxy. I get invalid password error. In addition, "User" and "Help" menu are not functioning. Thanks for any solution. -Sohail
Hello Sohail, Just as a start, if you have already followed the production server set up procedures, double check that you are using the email address (and not the user name) when logging into the UI form. If that does not solve the admin login issue, is likely that you need to do some more configuration in the universe_wsgi.ini file. Please see the sample in your download or at: http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.in... In particular, this section in universe_wsgi.ini will need to be set up: # -- Users and Security Start here: http://galaxyproject.org/Admin/Get Galaxy Then see: http://galaxyproject.org/Admin/Interface http://galaxyproject.org/Admin/Config/Performance/Production%20Server The two menu items that are not functioning are covered in the above configuration documentation or the universe_wsgi.ini.sample comments. Hopefully this helps, Best, Jen Galaxy team On 8/5/11 11:41 AM, sohkhan@notes.cc.sunysb.edu wrote:
Hi,
I have the admin user set in universe_wsgi.ini file, but I am unable to login to Galaxy. I get invalid password error. In addition, "User" and "Help" menu are not functioning. Thanks for any solution.
-Sohail
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Thanks Jennifer, I login with my e-mail,I have admin_users=my_email and admin_pass=my_password setup in universe_wsgi.ini. However, I am not sure if this correct. What is the admin password when you login for the first time? -Sohail From: Jennifer Jackson <jen@bx.psu.edu> To: sohkhan@notes.cc.sunysb.edu Cc: galaxy-dev@lists.bx.psu.edu Date: 08/09/2011 02:11 PM Subject: Re: [galaxy-dev] invalid password Hello Sohail, Just as a start, if you have already followed the production server set up procedures, double check that you are using the email address (and not the user name) when logging into the UI form. If that does not solve the admin login issue, is likely that you need to do some more configuration in the universe_wsgi.ini file. Please see the sample in your download or at: http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.in... In particular, this section in universe_wsgi.ini will need to be set up: # -- Users and Security Start here: http://galaxyproject.org/Admin/Get Galaxy Then see: http://galaxyproject.org/Admin/Interface http://galaxyproject.org/Admin/Config/Performance/Production%20Server The two menu items that are not functioning are covered in the above configuration documentation or the universe_wsgi.ini.sample comments. Hopefully this helps, Best, Jen Galaxy team On 8/5/11 11:41 AM, sohkhan@notes.cc.sunysb.edu wrote:
Hi,
I have the admin user set in universe_wsgi.ini file, but I am unable to login to Galaxy. I get invalid password error. In addition, "User" and "Help" menu are not functioning. Thanks for any solution.
-Sohail
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Hello Sohail, The universe_wsgi.ini for admin is correct. Have you registered through the UI yet? Once registered and logged in with these same credentials, the account should be granted admin permissions. Jen On 8/9/11 11:25 AM, sohkhan@notes.cc.sunysb.edu wrote:
Thanks Jennifer, I login with my e-mail,I have admin_users=my_email and admin_pass=my_password setup in universe_wsgi.ini. However, I am not sure if this correct. What is the admin password when you login for the first time? -Sohail
From: Jennifer Jackson <jen@bx.psu.edu> To: sohkhan@notes.cc.sunysb.edu Cc: galaxy-dev@lists.bx.psu.edu Date: 08/09/2011 02:11 PM Subject: Re: [galaxy-dev] invalid password ------------------------------------------------------------------------
Hello Sohail,
Just as a start, if you have already followed the production server set up procedures, double check that you are using the email address (and not the user name) when logging into the UI form.
If that does not solve the admin login issue, is likely that you need to do some more configuration in the universe_wsgi.ini file. Please see the sample in your download or at: http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.in...
In particular, this section in universe_wsgi.ini will need to be set up: # -- Users and Security
Start here: http://galaxyproject.org/Admin/GetGalaxy
Then see: http://galaxyproject.org/Admin/Interface http://galaxyproject.org/Admin/Config/Performance/Production%20Server
The two menu items that are not functioning are covered in the above configuration documentation or the universe_wsgi.ini.sample comments.
Hopefully this helps,
Best,
Jen Galaxy team
On 8/5/11 11:41 AM, sohkhan@notes.cc.sunysb.edu wrote:
Hi,
I have the admin user set in universe_wsgi.ini file, but I am unable to login to Galaxy. I get invalid password error. In addition, "User" and "Help" menu are not functioning. Thanks for any solution.
-Sohail
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org <http://usegalaxy.org/> http://galaxyproject.org/Support
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Hi Jennifer, Problem solved! I hadn't registered through UI..... Thanks for your help. -Sohail From: Jennifer Jackson <jen@bx.psu.edu> To: sohkhan@notes.cc.sunysb.edu Cc: galaxy-dev@lists.bx.psu.edu Date: 08/09/2011 02:48 PM Subject: Re: [galaxy-dev] invalid password Hello Sohail, The universe_wsgi.ini for admin is correct. Have you registered through the UI yet? Once registered and logged in with these same credentials, the account should be granted admin permissions. Jen On 8/9/11 11:25 AM, sohkhan@notes.cc.sunysb.edu wrote:
Thanks Jennifer, I login with my e-mail,I have admin_users=my_email and admin_pass=my_password setup in universe_wsgi.ini. However, I am not sure if this correct. What is the admin password when you login for the first time? -Sohail
From: Jennifer Jackson <jen@bx.psu.edu> To: sohkhan@notes.cc.sunysb.edu Cc: galaxy-dev@lists.bx.psu.edu Date: 08/09/2011 02:11 PM Subject: Re: [galaxy-dev] invalid password ------------------------------------------------------------------------
Hello Sohail,
Just as a start, if you have already followed the production server set up procedures, double check that you are using the email address (and not the user name) when logging into the UI form.
If that does not solve the admin login issue, is likely that you need to do some more configuration in the universe_wsgi.ini file. Please see the sample in your download or at:
http://bitbucket.org/galaxy/galaxy-central/src/1291bc31fec6/universe_wsgi.in...
In particular, this section in universe_wsgi.ini will need to be set up: # -- Users and Security
Start here: http://galaxyproject.org/Admin/GetGalaxy
Then see: http://galaxyproject.org/Admin/Interface http://galaxyproject.org/Admin/Config/Performance/Production%20Server
The two menu items that are not functioning are covered in the above configuration documentation or the universe_wsgi.ini.sample comments.
Hopefully this helps,
Best,
Jen Galaxy team
On 8/5/11 11:41 AM, sohkhan@notes.cc.sunysb.edu wrote:
Hi,
I have the admin user set in universe_wsgi.ini file, but I am unable
to
login to Galaxy. I get invalid password error. In addition, "User" and "Help" menu are not functioning. Thanks for any solution.
-Sohail
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org <http://usegalaxy.org/> http://galaxyproject.org/Support
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
participants (5)
-
Jennifer Jackson -
Joachim Jacob -
Nate Coraor -
Paul Gordon -
sohkhan＠notes.cc.sunysb.edu