Re: [galaxy-dev] missing slash when installing from toolshed?
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://%{HTTP_HOST}%{REQUEST_URI}
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 dansulli...@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 g...@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%202012-08-21%20at%203.22.27%20PM.png
Dan
On Aug 22, 2012, at 10:13 AM, Dan Sullivan dansulli...@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-td4353417.html
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%202012-08-21%20at%203.22.27%20PM.png
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
Re: [galaxy-dev] missing slash when installing from toolshed?
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 g...@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%202012-08-21%20at%203.22.27%20PM.png Dan On Aug 22, 2012, at 10:13 AM, Dan Sullivan dansulli...@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-td4353417.html 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%202012-08-21%20at%203.22.27%20PM.png 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/ ___ 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] missing slash when installing from toolshed?
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%202012-08-21%20at%203.22.27%20PM.png Dan On Aug 22, 2012, at 10:13 AM, Dan Sullivan dansulli...@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-td4353417.html 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%202012-08-21%20at%203.22.27%20PM.png 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/ ___ 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/
