Hi Dan,

The only thing I can think of that is causing this behavior is an apache rewrite rule that is not correctly handling your base URL. That's the only scenario in which I've seen something like this occur, but others in the community may have seen other causes. I'm fairly certain it has something to do with the server configuration (not a Galaxy issue).

Greg Von Kuster

On Aug 22, 2012, at 3:18 PM, Dan Sullivan wrote:

I apologize for spamming this list, the screenshot that I specified as "attached" was supplied in a hyperlink farther down in the mail (not as an attachment).

https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-...

Dan

On Aug 22, 2012, at 10:13 AM, Dan Sullivan dansullivan@gmail.com wrote:

...

Hi, Galaxy Developers,

I have a question that is very similar to the following thread;

http://dev.list.galaxyproject.org/Problem-fetching-updates-to-toolshed-tool-...

Basically whenever I try to install a tool from the toolshed, it appears that a trailing slash is not appended to the Galaxy URL, which is causing a DNS lookup failure. For example, the URL specified in the attached screenshot should be https://crigalaxy.uchicago.edu/admin_toolshed, however it is appearing as https://crigalaxy.uchicago.eduadmin_toolshed. Does anybody know if there are any known bugs that would cause this behavior? I might venture down the road of modifying lib/galaxy/webapps/community/controllers/repository.py as suggested by the thread above, although I would like to avoid doing this if possible. I am seeing experiencing this behavior on the following version of Galaxy:

...

hg parent

changeset: 7400:ec29ce8e27a1

In addition to this, I feel that its worthwhile to mention that I am using the apache proxy balancer with web scaling, however based on what I have seen and tested, I do not believe this (apache) to be the root cause of my problem. The URL below is a screenshot of the network debug I am seeing from the firebug extension in firefox.

https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-...

If somebody has seen this, or could offer a suggestion to bring this issue to resolve, I would definitely be interested in your strategy. Thank-you so much for your help and for your time.

Dan Sullivan 312-607-3702

---

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Hi, Galaxy Developers,

This is just a follow up to my previous response; I was able to get things working, and have pasted our apache configuration below for anybody else that search the mailing list with similar problems. Our implementation authenticates against UNIX LDAP and use a group for authorization. So far we have not had any problems with the following configuration ( I realize this is already similar to what is posted on the wiki). Thank-you again for your help, Greg.

RewriteEngine On RewriteCond %{HTTPS} off RewriteRule (.*) https://%%7BHTTP_HOST%7D%%7BREQUEST_URI%7D

<VirtualHost *:443> LoadModule ssl_module modules/mod_ssl.so ServerName crigalaxy.uchicago.edu SSLEngine On SSLCertificateFile /group/galaxy/certs/crigalaxy.cer SSLCertificateKeyFile /group/galaxy/certs/crigalaxy.key SSLCertificateChainFile /group/galaxy/certs/crigalaxy_interm.cer <Location "/"> Authtype Basic AuthName Galaxy AuthBasicProvider ldap AuthLDAPURL "ldap://someldapserver.whateverdomain.edu:389/dc=uchicago,dc=edu?uid?sub?(objectClass=inetOrgPerson)" TLS AuthzLDAPAuthoritative off Require ldap-group cn=uc:org:cri:galaxy:cri-galaxy_web_users,ou=groups,dc=uchicago,dc=edu RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e </Location> RewriteEngine on <Proxy balancer://galaxy/> BalancerMember http://127.0.0.1:8080 BalancerMember http://127.0.0.1:8081 </Proxy> RewriteRule ^/static/style/(.*) /group/galaxy/galaxy-dist/static/uchicago_cri_august_2012_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /group/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /group/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/robots.txt /group/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) balancer://galaxy$1 [P] </VirtualHost>

Dan Sullivan

On Aug 29, 2012, at 9:44 AM, Daniel Patrick Sullivan dansullivan@gmail.com wrote:

Hi, Greg,

Thank-you so much for taking the time to answer my question. You appear to be correct; I removed the virtual hosting configuration from apache (I had some redirection configured to automatically forward from port 80 to port 443), and this problem went away. I think I should be able to get things situated from here (I'll try to remember to publish my working config when I get things worked out for for the people that use the mail archive). Again, thank-you for your time and expertise.

Dan Sullivan

On Tue, Aug 28, 2012 at 5:10 PM, Greg Von Kuster greg@bx.psu.edu wrote:

...

Hi Dan,

The only thing I can think of that is causing this behavior is an apache rewrite rule that is not correctly handling your base URL. That's the only scenario in which I've seen something like this occur, but others in the community may have seen other causes. I'm fairly certain it has something to do with the server configuration (not a Galaxy issue).

Greg Von Kuster

On Aug 22, 2012, at 3:18 PM, Dan Sullivan wrote:

I apologize for spamming this list, the screenshot that I specified as "attached" was supplied in a hyperlink farther down in the mail (not as an attachment).

https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-...

Dan

On Aug 22, 2012, at 10:13 AM, Dan Sullivan dansullivan@gmail.com wrote:

Hi, Galaxy Developers,

I have a question that is very similar to the following thread;

http://dev.list.galaxyproject.org/Problem-fetching-updates-to-toolshed-tool-...

Basically whenever I try to install a tool from the toolshed, it appears that a trailing slash is not appended to the Galaxy URL, which is causing a DNS lookup failure. For example, the URL specified in the attached screenshot should be https://crigalaxy.uchicago.edu/admin_toolshed, however it is appearing as https://crigalaxy.uchicago.eduadmin_toolshed. Does anybody know if there are any known bugs that would cause this behavior? I might venture down the road of modifying lib/galaxy/webapps/community/controllers/repository.py as suggested by the thread above, although I would like to avoid doing this if possible. I am seeing experiencing this behavior on the following version of Galaxy:

...

hg parent

changeset: 7400:ec29ce8e27a1

In addition to this, I feel that its worthwhile to mention that I am using the apache proxy balancer with web scaling, however based on what I have seen and tested, I do not believe this (apache) to be the root cause of my problem. The URL below is a screenshot of the network debug I am seeing from the firebug extension in firefox.

https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-...

If somebody has seen this, or could offer a suggestion to bring this issue to resolve, I would definitely be interested in your strategy. Thank-you so much for your help and for your time.

Dan Sullivan 312-607-3702

---

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/