Re: [galaxy-dev] Apache configuration problem
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 To: joachim.ja...@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-boun...@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 Order deny,allow Allow from all 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/ ___ 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] Apache configuration problem
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, sohk...@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 To: joachim.ja...@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-boun...@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 Order deny,allow Allow from all 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: _http://lists.bx.psu.edu/_ -- __ 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: 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/
Re: [galaxy-dev] Apache configuration problem
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 Order deny,allow Allow from all 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/
Re: [galaxy-dev] Apache configuration problem?
I Running run.sh as root helped me get rid of the permission denied errors. After modifying the apache and galaxy config files, restart the apache web server then run the run.sh as root $ sudo su root $ source galaxy_env/bin/activate $ sh galaxy_dist/run.sh Hope this helps Lucie --- Lucie Hutchins Scientific Software Engineer The Jackson Laboratory Email: lucie.hutch...@jax.og web: harlequin.jax.org Phone: 1-207-288-6764 From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Yu Wang [yu.w...@wzw.tum.de] Sent: Tuesday, April 12, 2011 4:13 PM To: di...@immunbio.mpg.de Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Apache configuration problem? hi, sarah, sorry for the confusion. I did change those lines with my own directories. And the files are readable for others. Regards, Yu Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.w...@wzw.tum.de D-85354 Freising Germany ___ 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/
Re: [galaxy-dev] Apache configuration problem?
hi, sarah, sorry for the confusion. I did change those lines with my own directories. And the files are readable for others. Regards, Yu Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.w...@wzw.tum.de D-85354 Freising Germany ___ 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] Apache configuration problem?
Hello Yu, first, you need to change the /home/nate/galaxy_dist in the rewrite rules to the directory on your machine where the galaxy files are. Second, I think the apache user needs at least read access to the static directory inside the galaxy directory. Regards, Sarah On 04/12/2011 04:11 PM, Yu Wang wrote: Hello, I installed Galaxy on Fedora 13. Everything works fine at http://127.0.0.1:8080 Then I followed instruction from https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. I add the following lines to httpd.conf: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/nate/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/nate/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/nate/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/nate/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] and changed universe_wsgi.ini with [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy I restarted Apache and Galaxy. At http://127.0.0.1:8080 everything works fine but at http://xx.xx.xx.xx/galaxy I got a scrambled page. Apache error log said "[Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/style/base.css denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/style/tool_menu.css denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/scripts/jquery.js denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/scripts/galaxy.base.js denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu " Can anyone point out what was configured wrong? Many thanks in advance. Best regards, Yu Wang Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.w...@wzw.tum.de D-85354 Freising Germany ___ 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/
