[galaxy-dev] Galaxy, Apache, WSGI and mod_wsgi

2012-10-22 Thread Paul Boddie
Hello, I have recently had the opportunity to look at the deployment of Galaxy together with Apache, and I saw that the recommendation is to run the Galaxy Web server behind Apache with the latter acting as a proxy: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy Other than

Re: [galaxy-dev] Galaxy, Apache, WSGI and mod_wsgi

2012-10-24 Thread Paul Boddie
On 24/10/12 18:09, Carl Eberhard wrote: I would like to know if mod_wsgi has been considered for the deployment of Galaxy at all, and whether anyone has any positive or negative experiences with it. I can only speak for the second part of your question: I've had some experience with Apache 2

Re: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known

2012-11-05 Thread Paul Boddie
On 04/11/12 16:39, Marcelo Timmerman wrote: Nobody? Anyone knows if using nginx would avoid the internal HTTP Python server? It appears that nginx is used as a proxy in front of the Python/Paste server, not as a replacement. You could use something like mod_wsgi with Apache instead of that

Re: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known

2012-11-07 Thread Paul Boddie
On 06/11/12 23:37, Marcelo Timmerman wrote: Agree. But the fact that you cannot easily rapidly debug the failing expression is dissapointing. A backtrace is a lot better than Segmentation fault. Maybe there should be an exception handler that displays a nice message, but then there's the

Re: [galaxy-dev] Problem with Active Directory/LDAP authentication

2012-11-28 Thread Paul Boddie
On 28/11/12 06:12, Harris Shapiro wrote: 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

Re: [galaxy-dev] Required Galaxy umask settings for HTML downloads?

2012-12-04 Thread Paul Boddie
On 04/12/12 16:52, Josh Nielsen wrote: I am getting the error (13)Permission denied: xsendfile: cannot open file: /basedir/galaxy_data/database/tmp/tmp8iEccn/library_download.zip which is indeed a basic filesystem permissions issue. The problem is that the permissions created for that directory

Re: [galaxy-dev] Required Galaxy umask settings for HTML downloads?

2012-12-04 Thread Paul Boddie
On 04/12/12 17:35, Josh Nielsen wrote: Hi Paul, Thanks for replying. Interestingly I've never dealt with filesystem ACLs before and I didn't even know that ext3/4 systems had that feature. Here is my output from those commands: bash getfacl tmp8iEccn # file: tmp8iEccn # owner: galaxy #

[galaxy-dev] Redirecting to a URL and breaking the frameset

2013-01-21 Thread Paul Boddie
Hello, Is there a convenient recipe for redirecting to a URL and breaking the frameset? I have been trying to use trans.response.send_redirect with a variety of URLs, either something as simple as url_for(/) or as complicated as a url_for invocation with lots of arguments, but the resulting

Re: [galaxy-dev] Redirecting to a URL and breaking the frameset

2013-01-21 Thread Paul Boddie
On 21/01/13 15:16, Jeremy Goecks wrote: Adding the attribute target=_top to your URL will load the URL in the main browser window rather than a frame. E.g. a href=controller/action target=_topLoad result in top window/a But in the Python code itself? I'm writing an action in the user

Re: [galaxy-dev] Redirecting to a URL and breaking the frameset

2013-01-21 Thread Paul Boddie
On 21/01/13 15:26, Paul Boddie wrote: On 21/01/13 15:16, Jeremy Goecks wrote: Adding the attribute target=_top to your URL will load the URL in the main browser window rather than a frame. E.g. a href=controller/action target=_topLoad result in top window/a But in the Python code itself

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Paul Boddie
On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which

Re: [galaxy-dev] Fwd: Desire to contribute

2013-02-08 Thread Paul Boddie
On 06/02/13 20:23, Dave Clements wrote: Please let the list know if any of the ideas posted so far grab you, or if you want further explanation. Thanks for your interest and for picking the Galaxy Project. Efforts like these really help the project move forward. Are there any lists that are

Re: [galaxy-dev] Authentication: email addresses are not validated prior to account creation

2013-03-05 Thread Paul Boddie
On 05/03/13 17:09, James Taylor wrote: On Mar 1, 2013, at 10:39 AM, Vipin TS vipin...@gmail.com wrote: Hello members, I believe currently there is no process to validate email address provided during user account creation. We are experiencing a huge fake account creation attack on our

Re: [galaxy-dev] Serving Galaxy behind apache mod_security

2013-03-12 Thread Paul Boddie
On 11/03/13 23:20, Vipin TS wrote: On my new server machine I have configured apache server along with mod_security. Now I would like to place my Galaxy installation behind apache and is there any detailed explanation to describes the steps. I am following the galaxy wiki