Hello,
Thanks to everyone for the feedback and suggestions. I was eventually
able to puzzle out what was going awry. The remaining issues turned out
to be:
1) When proxying was enabled, to trigger an authentication request with
the default Galaxy set-up, I needed to use the “localhost” URL, instead
of “localhost:8080”. I guess I might have missed the documentation for
this...
2) Overly aggressive “Security-Enhanced Linux” settings, which were
silently blocking some of the needed HTTP communication. I never did
find any log messages for this; I just guessed it might be an issue and
turned it off. Everything then happily started working...
Anyway, thanks again for the responses and example configuration.
Harris
On 11/27/12 12:08 PM, Carlos Borroto wrote:
Hi Harris,
I can't pin-point your issue exactly, to be honest I don't quite
remember how I got to this working configuration. Still please take a
look at this configuration as I'm using it in almost exactly the same
enviroment, Centos 6/Apache 2.2.15/Active Directory...
<VirtualHost *:80>
ServerAdmin admin@local
ServerName galaxy.local:80
<Proxy http://localhost:8080>
Order deny,allow
Allow from all
</Proxy>
RewriteEngine on
<Location "/">
AuthName "Galaxy BFX"
AuthType Basic
AuthBasicAuthoritative off
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPURL [LDAP_URL]
AuthLDAPBindDN [DN]
AuthLDAPBindPassword [PW]
Require valid-user
# Set the REMOTE_USER header to the contents of the LDAP query
response's "uid" attribute
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
XSendFile on
XSendFilePath /
</Location>
RewriteRule ^/static/style/(.*)
/local/opt/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/local/opt/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /local/opt/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico
/local/opt/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /local/opt/galaxy/galaxy-dist/static/robots.txt
[L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
ErrorLog logs/galaxy.local-error_log
CustomLog logs/galaxy.local-access_log common
</VirtualHost>
Cheers,
Carlos
On Mon, Nov 19, 2012 at 12:49 PM, Harris Shapiro <hjshap...@gmail.com> wrote:
Hello,
I'm writing because I've been trying for the past few days to configure
Galaxy to use Apache-based LDAP authentication, but have reached a point
where I'm basically stuck. The system in a virtual machine running:
- CentOS 5.8
- Apache 2.2.3
I'm trying to configure a Galaxy instance at "localhost:8080", with Active
Directory authentication.
I started with the admin page documentation:
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy
and also worked through the troubleshooting examples found at:
a)
http://user.list.galaxyproject.org/Galaxy-Apache-External-Authentication-tt4131493.html#a4131495
b)
http://gmod.827538.n3.nabble.com/galaxy-dev-ldap-integration-td839409.html
c) http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-January/001676.html
Following the debugging steps suggested by URL (a), I'm able to verify that:
1) The authentication clause I have works, without rewrite rules and without
a proxy.
2) Without rewrite rules and a proxy, the Apache environment has the
AUTHENTICATE_SAMACCOUNTNAME and REMOTE_USER environment variables set.
Unfortunately, when I turn on the proxy (setting "use_remote_user" and
"remote_user_maildomain" in universe_wsgi.ini accordingly), I get the
following error message when I try accessing the "localhost:8080" URL, the
following error message appears:
"Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as
HTTP authentication in Apache), but a username was not provided by the
upstream (proxy) server. This is generally due to a misconfiguration in the
upstream server.
Please contact your local Galaxy administrator."
As suggested by URLs (a) and (c), I modified
./lib/galaxy/web/framework/middleware/remoteuser.py to print the environment
seen by that script. None of the remote user information seems to be making
to the script, either from AUTHENTICATE_SAMACCOUNTNAME or REMOTE_USER, no
matter which of the suggested combinations of "RewriteCond", "RewriteRule",
and "RequestHeader" options I tried. In addition, the troubleshooting
suggestions to force a REMOTE_USER value to be set via a directive like:
RequestHeader add REMOTE_USER [user name]
also failed to pass REMOTE_USER to the remoteuser.py script.
I've included below an extract from the Apache configuration file that I've
been trying. Any advice or assistance that people might be able to provide
would be greatly appreciated, and please let me know if you'd need any
additional information from me.
Sincerely,
Harris Shapiro
Genomic Health, Inc.
Extract from Apache configuration file:
Note: I've also tried a variant where I replaced REMOTE_USER with
AUTHENTICATE_SAMACCOUNTNAME in the various RewriteCond & RequestHeader
directives. That variant produced the same error message.
<Proxy http://localhost:8080>
Order deny,allow
Allow from all
</Proxy>
RewriteEngine on
<Location "/">
AuthType Basic
AuthName "Please log in with your Windows account"
AuthBasicProvider ldap
AuthLDAPURL [Verified LDAP connection information]
AuthzLDAPAuthoritative off
AuthLDAPBindDN [Verified DN]
AuthLDAPBindPassword [Verified password]
Require valid-user
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
</Location>
RewriteRule ^/static/style/(.*)
/home/hshapiro/software/galaxy/galaxy-dist/static/june_2007_style/blue/$1
[L]
RewriteRule ^/static/scripts/(.*)
/home/hshapiro/software/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*)
/home/hshapiro/software/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico
/home/hshapiro/software/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt
/home/hshapiro/software/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
___________________________________________________________
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/
