Re: [galaxy-dev] Installing Cairo into Gakaxy

2015-10-13 Thread Christian Brenninkmeijer
Thanks all for the help, Using Marius's Cairo https://testtoolshed.g2.bx.psu.edu/view/mvdbeek/package_cairo_1_14_2/83f00b68affb And a slightly changed R https://testtoolshed.g2.bx.psu.edu/view/brenninc/brenninc_r_sept32105/83005a26c16f This is based on:

Re: [galaxy-dev] Galaxy Interactive Environment devs

2015-10-13 Thread Sebastian Schaaf
Hey Eric, We are not yet on IEs, but we plan to upgrade our local production instance soon (a recent version is already 'waiting' to take over), apart from other goodies we intended to allow one pro user and ourselves to use iPython's power this way. So, do I read your message correctly as

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

2015-10-13 Thread Sebastian Schaaf
Hey there, Any news on this? My colleague Aarif made me aware of the discussion, because one of our students, Ashok, worked on this months ago. QIIME was requested by a project which never started and therefore the developed codes did not gain priority. Basically we faced the same issues,

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Eric Rasche
Hi Ryan, On 10/13/2015 09:50 AM, Ryan G wrote: > Hi all - In regards to external user authentication that I have working > now (see thread below). When users try to go to the actual Galaxy page, > they get the message: > > > Access to Galaxy is denied That's expected for External User

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Eric Rasche
On 10/13/2015 11:34 AM, Ryan G wrote: > We have Apache set up to authenticate users off our LDAP. If they > authenticate correctly, they are then forwarded on through the proxy. So, mod_auth_ldap? Or not? You say "forwarded" so I'm thinking you may not mean this. > > What I want is to

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Ryan G
Sorry, maybe I'm not being clear. Galaxy is listening on http://galaxy.mycompany.com:8080 Users access Galaxy via http://mycompay.com/galaxy If users go to http://galaxy.mycompany.com:8080, they get the External Authentication message. From here I want them to be redirected to

[galaxy-dev] MS Active Directory Authentication

2015-10-13 Thread McCully, Dwayne (NIH/NIAMS) [C]
Hello Everyone, Is there an example of the auth_config.xml for a MS Active directory connection? I would like to all my users to register and login to Galaxy with their AD username and password. Note: We don't use a "@example.com" extension for our usernames just "username". Thanks in advance

Re: [galaxy-dev] MS Active Directory Authentication

2015-10-13 Thread Nicola Soranzo
Hi Dwayne, see https://github.com/galaxyproject/galaxy/blob/dev/config/auth_conf.xml.sample ldap is equivalent to activedirectory Something like this may work for you: activedirectory False True ldap://dc1.example.com True

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Eric Rasche
Howdy Ryan, On 10/13/2015 11:44 AM, Ryan G wrote: > Sorry, maybe I'm not being clear. > > Galaxy is listening on http://galaxy.mycompany.com:8080 > > Users access Galaxy via http://mycompay.com/galaxy Ah! This is much more clear, thanks :) If you're running under remote_user, you should NOT

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Ryan G
We have Apache set up to authenticate users off our LDAP. If they authenticate correctly, they are then forwarded on through the proxy. What I want is to prevent users from hitting the galaxy URL directly. If they, do I want to automatically redirect them to the proxy. On Tue, Oct 13, 2015 at

Re: [galaxy-dev] Galaxy Interactive Environment devs

2015-10-13 Thread Eric Rasche
Hey Sebastian On 10/13/2015 06:41 AM, Sebastian Schaaf wrote: > Hey Eric, > > We are not yet on IEs, but we plan to upgrade our local production > instance soon (a recent version is already 'waiting' to take over), > apart from other goodies we intended to allow one pro user and ourselves > to

Re: [galaxy-dev] MS Active Directory Authentication

2015-10-13 Thread McCully, Dwayne (NIH/NIAMS) [C]
Thanks Nicola, Updated the auth_config.xml file but got the following message in the paster.log. Any idea how to fix? DEBUG 2015-10-13 14:18:11,644 LDAP authenticate: could not load ldap module Dwayne From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola Soranzo Sent:

[galaxy-dev] CORS requests to public Galaxy server

2015-10-13 Thread Marco Ocana
Hi, I am attempting to access the public usegalaxy.org server using the REST API from web browsers. The question: I am not seeing Access-Control-Allow-* headers in REST API responses. Are browser REST CORS requests supported by the Galaxy servers? More details: Here is an error reported by

Re: [galaxy-dev] MS Active Directory Authentication

2015-10-13 Thread Nicola Soranzo
Hi Dwayne, you need to install the Python LDAP module: http://www.python-ldap.org/ https://pypi.python.org/pypi/python-ldap/ If you are using a virtualenv (which is recommended for a production server), activate it and then execute: pip install ldap Cheers, Nicola Il giorno mar, 13/10/2015