Galaxy server configuration question
Dear Sir or Madam, I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? Best, Huayan
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate
Best, Huayan ___________________________________________________________ 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 Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? Thanks, Best, Huayan On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
Best, Huayan ___________________________________________________________ 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 Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, "the file .../static/welcome.html is missing" or something like that. Thanks, Huayan On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
Best, Huayan ___________________________________________________________ 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 Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved. Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
Best, Huayan ___________________________________________________________ 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:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
Best, Huayan ___________________________________________________________ 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:
Good point, Nate! I will move galaxy out of my documentroot then. Best, Huayan On Tue, Feb 14, 2012 at 1:21 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
Best, Huayan ___________________________________________________________ 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:
Dear Nate, I have a follow up question for you. If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck. Best, Huayan On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
Best, Huayan ___________________________________________________________ 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:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan, The configuration for this is shown under the heading: Serving Galaxy at a sub directory (such as /galaxy) On the Apache Proxy wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy --nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
> Dear Sir or Madam, > > I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. > Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?
Hi Huayan,
Have you consulted the production server documentation?
http://usegalaxy.org/production
--nate
> > > > Best, > Huayan > ___________________________________________________________ > 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/
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/... Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh I could not figure it out what is wrong. Any suggestions? Best, Huayan On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
Hi Nate,
Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks, Best, Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: > >> Dear Sir or Madam, >> >> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? > > Hi Huayan, > > Have you consulted the production server documentation? > > http://usegalaxy.org/production > > --nate > >> >> >> >> Best, >> Huayan >> ___________________________________________________________ >> 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/ >
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan, Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist. --nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
Hi Nate,
I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it?
It seems to say, "the file .../static/welcome.html is missing" or something like that.
Thanks, Huayan
<Screen Shot 2012-02-13 at 11.37.57 AM.png>
On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
> Hi Nate, > > > Yes, I did follow the instructions. But I came to the question in httpd.conf file. > I put galaxy-dist under my document root which is /var/www/html/. > When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. > Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? > > > > > Thanks, > Best, > Huayan > > > > > On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: > >> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >> >>> Dear Sir or Madam, >>> >>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >> >> Hi Huayan, >> >> Have you consulted the production server documentation? >> >> http://usegalaxy.org/production >> >> --nate >> >>> >>> >>> >>> Best, >>> Huayan >>> ___________________________________________________________ >>> 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/ >> >
Dear Nate, Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working. Could it possible to send me your httpd.conf file for reference? Best, Huayan On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan,
Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist.
--nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
Best, Huayan
On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
> Hi Nate, > > I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. > I will keep looking for the solution but do you know how to fix it? > > It seems to say, "the file .../static/welcome.html is missing" or something like that. > > Thanks, > Huayan > > > > > <Screen Shot 2012-02-13 at 11.37.57 AM.png> > > > > On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: > >> Hi Nate, >> >> >> Yes, I did follow the instructions. But I came to the question in httpd.conf file. >> I put galaxy-dist under my document root which is /var/www/html/. >> When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. >> Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? >> >> >> >> >> Thanks, >> Best, >> Huayan >> >> >> >> >> On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: >> >>> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >>> >>>> Dear Sir or Madam, >>>> >>>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >>> >>> Hi Huayan, >>> >>> Have you consulted the production server documentation? >>> >>> http://usegalaxy.org/production >>> >>> --nate >>> >>>> >>>> >>>> >>>> Best, >>>> Huayan >>>> ___________________________________________________________ >>>> 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/ >>> >> >
On May 18, 2012, at 2:37 AM, Huayan Gao wrote:
Dear Nate,
Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working.
Could it possible to send me your httpd.conf file for reference?
Best, Huayan
Hi Huayan, I don't have Galaxy running behind Apache here, so I don't have a full example to send. Can you check that all of the directories: /home /home/galaxy /home/galaxy/galaxy-dist /home/galaxy/galaxy-dist/static Are accessible by the user that Apache runs as? In addition, check that a <Directory> directives that would cover /home/galaxy/galaxy-dist/static do not contain "Deny from all", Many configurations by default have an entry like: <Directory /> Some options... Deny from all </Directory> You would need to add something like: <Directory "/home/galaxy/galaxy-dist/static"> Order deny,allow Allow from all </Directory> --nate
On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan,
Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist.
--nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
> Hi Nate. > > I am ok now. > > The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. > After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
> > > > Best, > Huayan > > > On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: > >> Hi Nate, >> >> I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. >> I will keep looking for the solution but do you know how to fix it? >> >> It seems to say, "the file .../static/welcome.html is missing" or something like that. >> >> Thanks, >> Huayan >> >> >> >> >> <Screen Shot 2012-02-13 at 11.37.57 AM.png> >> >> >> >> On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: >> >>> Hi Nate, >>> >>> >>> Yes, I did follow the instructions. But I came to the question in httpd.conf file. >>> I put galaxy-dist under my document root which is /var/www/html/. >>> When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. >>> Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? >>> >>> >>> >>> >>> Thanks, >>> Best, >>> Huayan >>> >>> >>> >>> >>> On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: >>> >>>> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >>>> >>>>> Dear Sir or Madam, >>>>> >>>>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>>>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >>>> >>>> Hi Huayan, >>>> >>>> Have you consulted the production server documentation? >>>> >>>> http://usegalaxy.org/production >>>> >>>> --nate >>>> >>>>> >>>>> >>>>> >>>>> Best, >>>>> Huayan >>>>> ___________________________________________________________ >>>>> 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 Nate, Thanks for helping. I've tried this part already but it is still not working. Still scratching my head here....... Best, Huayan On 18 May, 2012, at 9:41 PM, Nate Coraor wrote:
On May 18, 2012, at 2:37 AM, Huayan Gao wrote:
Dear Nate,
Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working.
Could it possible to send me your httpd.conf file for reference?
Best, Huayan
Hi Huayan,
I don't have Galaxy running behind Apache here, so I don't have a full example to send.
Can you check that all of the directories:
/home /home/galaxy /home/galaxy/galaxy-dist /home/galaxy/galaxy-dist/static
Are accessible by the user that Apache runs as?
In addition, check that a <Directory> directives that would cover /home/galaxy/galaxy-dist/static do not contain "Deny from all", Many configurations by default have an entry like:
<Directory /> Some options... Deny from all </Directory>
You would need to add something like:
<Directory "/home/galaxy/galaxy-dist/static"> Order deny,allow Allow from all </Directory>
--nate
On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan,
Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist.
--nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
> On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: > >> Hi Nate. >> >> I am ok now. >> >> The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. >> After I changed the path in the code, the problem solved. > > Hi Huayan, > > I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. > > I would suggest moving galaxy out of /var/www/html. From the documentation: > > Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. > > Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. > > --nate > >> >> >> >> Best, >> Huayan >> >> >> On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: >> >>> Hi Nate, >>> >>> I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. >>> I will keep looking for the solution but do you know how to fix it? >>> >>> It seems to say, "the file .../static/welcome.html is missing" or something like that. >>> >>> Thanks, >>> Huayan >>> >>> >>> >>> >>> <Screen Shot 2012-02-13 at 11.37.57 AM.png> >>> >>> >>> >>> On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: >>> >>>> Hi Nate, >>>> >>>> >>>> Yes, I did follow the instructions. But I came to the question in httpd.conf file. >>>> I put galaxy-dist under my document root which is /var/www/html/. >>>> When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. >>>> Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? >>>> >>>> >>>> >>>> >>>> Thanks, >>>> Best, >>>> Huayan >>>> >>>> >>>> >>>> >>>> On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: >>>> >>>>> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >>>>> >>>>>> Dear Sir or Madam, >>>>>> >>>>>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>>>>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >>>>> >>>>> Hi Huayan, >>>>> >>>>> Have you consulted the production server documentation? >>>>> >>>>> http://usegalaxy.org/production >>>>> >>>>> --nate >>>>> >>>>>> >>>>>> >>>>>> >>>>>> Best, >>>>>> Huayan >>>>>> ___________________________________________________________ >>>>>> 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/ >>>>> >>>> >>> >> >
On May 21, 2012, at 8:59 PM, Huayan Gao wrote:
Hi Nate,
Thanks for helping. I've tried this part already but it is still not working.
Still scratching my head here.......
Hi Huayan, Unfortunately, there's not much else I can do - Apache is unable to access the files, either through a configuration directive or because it does not have permission on the filesystem. It's possible that I could spot the issue if you provided all of your Apache configuration files, but this is a problem that is a bit out of the scope of configuring Galaxy. Also, I am not sure how running Galaxy as root would alleviate the problem, since it seems to be that Apache can't access Galaxy's static files, and does not concern the Galaxy built-in web server. --nate
Best, Huayan
On 18 May, 2012, at 9:41 PM, Nate Coraor wrote:
On May 18, 2012, at 2:37 AM, Huayan Gao wrote:
Dear Nate,
Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working.
Could it possible to send me your httpd.conf file for reference?
Best, Huayan
Hi Huayan,
I don't have Galaxy running behind Apache here, so I don't have a full example to send.
Can you check that all of the directories:
/home /home/galaxy /home/galaxy/galaxy-dist /home/galaxy/galaxy-dist/static
Are accessible by the user that Apache runs as?
In addition, check that a <Directory> directives that would cover /home/galaxy/galaxy-dist/static do not contain "Deny from all", Many configurations by default have an entry like:
<Directory /> Some options... Deny from all </Directory>
You would need to add something like:
<Directory "/home/galaxy/galaxy-dist/static"> Order deny,allow Allow from all </Directory>
--nate
On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan,
Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist.
--nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
> Dear Nate, > > I have a follow up question for you. > > If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? > I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
> > > Best, > Huayan > > > > On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote: > >> On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: >> >>> Hi Nate. >>> >>> I am ok now. >>> >>> The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. >>> After I changed the path in the code, the problem solved. >> >> Hi Huayan, >> >> I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. >> >> I would suggest moving galaxy out of /var/www/html. From the documentation: >> >> Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. >> >> Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. >> >> --nate >> >>> >>> >>> >>> Best, >>> Huayan >>> >>> >>> On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: >>> >>>> Hi Nate, >>>> >>>> I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. >>>> I will keep looking for the solution but do you know how to fix it? >>>> >>>> It seems to say, "the file .../static/welcome.html is missing" or something like that. >>>> >>>> Thanks, >>>> Huayan >>>> >>>> >>>> >>>> >>>> <Screen Shot 2012-02-13 at 11.37.57 AM.png> >>>> >>>> >>>> >>>> On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: >>>> >>>>> Hi Nate, >>>>> >>>>> >>>>> Yes, I did follow the instructions. But I came to the question in httpd.conf file. >>>>> I put galaxy-dist under my document root which is /var/www/html/. >>>>> When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. >>>>> Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? >>>>> >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> Best, >>>>> Huayan >>>>> >>>>> >>>>> >>>>> >>>>> On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: >>>>> >>>>>> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >>>>>> >>>>>>> Dear Sir or Madam, >>>>>>> >>>>>>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>>>>>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >>>>>> >>>>>> Hi Huayan, >>>>>> >>>>>> Have you consulted the production server documentation? >>>>>> >>>>>> http://usegalaxy.org/production >>>>>> >>>>>> --nate >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Best, >>>>>>> Huayan >>>>>>> ___________________________________________________________ >>>>>>> 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/ >>>>>> >>>>> >>>> >>> >> > >
On May 18, 2012, at 1:37 AM, Huayan Gao wrote:
Dear Nate,
Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working.
Could it possible to send me your httpd.conf file for reference?
Best, Huayan
Huayan, The permission denied error might be coming because of selinux setting. If you have selinux in enforcing mode then try either of these options: 1. set selinux in permissive or disabled mode 2. modify selinux context on related files HTH.. -- Shantanu
On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan,
Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist.
--nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
> Hi Nate. > > I am ok now. > > The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. > After I changed the path in the code, the problem solved.
Hi Huayan,
I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion.
I would suggest moving galaxy out of /var/www/html. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly.
--nate
> > > > Best, > Huayan > > > On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: > >> Hi Nate, >> >> I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. >> I will keep looking for the solution but do you know how to fix it? >> >> It seems to say, "the file .../static/welcome.html is missing" or something like that. >> >> Thanks, >> Huayan >> >> >> >> >> <Screen Shot 2012-02-13 at 11.37.57 AM.png> >> >> >> >> On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: >> >>> Hi Nate, >>> >>> >>> Yes, I did follow the instructions. But I came to the question in httpd.conf file. >>> I put galaxy-dist under my document root which is /var/www/html/. >>> When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. >>> Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? >>> >>> >>> >>> >>> Thanks, >>> Best, >>> Huayan >>> >>> >>> >>> >>> On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: >>> >>>> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >>>> >>>>> Dear Sir or Madam, >>>>> >>>>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>>>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >>>> >>>> Hi Huayan, >>>> >>>> Have you consulted the production server documentation? >>>> >>>> http://usegalaxy.org/production >>>> >>>> --nate >>>> >>>>> >>>>> >>>>> >>>>> Best, >>>>> Huayan >>>>> ___________________________________________________________ >>>>> 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:
Hi Shantanu, I checked the status of SELinux, it is disabled. [root@galaxy ~]# sestatus SELinux status: disabled Not sure where I went wrong. Right now I am running Galaxy under root. Best, Huayan On 18 May, 2012, at 10:19 PM, Shantanu Pavgi wrote:
On May 18, 2012, at 1:37 AM, Huayan Gao wrote:
Dear Nate,
Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working.
Could it possible to send me your httpd.conf file for reference?
Best, Huayan
Huayan,
The permission denied error might be coming because of selinux setting. If you have selinux in enforcing mode then try either of these options: 1. set selinux in permissive or disabled mode 2. modify selinux context on related files
HTH..
-- Shantanu
On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, "Forbidden……You don't have permission to access /galaxy/static/welcome.html…." I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/...
Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history
Hi Huayan,
Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or <Directory> directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist.
--nate
I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best, Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck.
Hi Huayan,
The configuration for this is shown under the heading:
Serving Galaxy at a sub directory (such as /galaxy)
On the Apache Proxy wiki page:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
--nate
Best, Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
> On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: > >> Hi Nate. >> >> I am ok now. >> >> The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. >> After I changed the path in the code, the problem solved. > > Hi Huayan, > > I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. > > I would suggest moving galaxy out of /var/www/html. From the documentation: > > Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. > > Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. > > --nate > >> >> >> >> Best, >> Huayan >> >> >> On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: >> >>> Hi Nate, >>> >>> I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. >>> I will keep looking for the solution but do you know how to fix it? >>> >>> It seems to say, "the file .../static/welcome.html is missing" or something like that. >>> >>> Thanks, >>> Huayan >>> >>> >>> >>> >>> <Screen Shot 2012-02-13 at 11.37.57 AM.png> >>> >>> >>> >>> On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: >>> >>>> Hi Nate, >>>> >>>> >>>> Yes, I did follow the instructions. But I came to the question in httpd.conf file. >>>> I put galaxy-dist under my document root which is /var/www/html/. >>>> When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. >>>> Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? >>>> >>>> >>>> >>>> >>>> Thanks, >>>> Best, >>>> Huayan >>>> >>>> >>>> >>>> >>>> On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: >>>> >>>>> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: >>>>> >>>>>> Dear Sir or Madam, >>>>>> >>>>>> I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. >>>>>> Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? >>>>> >>>>> Hi Huayan, >>>>> >>>>> Have you consulted the production server documentation? >>>>> >>>>> http://usegalaxy.org/production >>>>> >>>>> --nate >>>>> >>>>>> >>>>>> >>>>>> >>>>>> Best, >>>>>> Huayan >>>>>> ___________________________________________________________ >>>>>> 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/ >>>>> >>>> >>> >> >
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participants (4)
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huayan gao -
Huayan Gao
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Nate Coraor -
Shantanu Pavgi