Hi Peter,
Thank you for the prompt reply and the clear answer!
Indeed, I don't want to ask for more than what I need (i.e., sudo) since that would scare a lot of people. However, I'd like to strike a balance and be able to help users without pestering the system administrators too much.
With administrator rights to just the Galaxy interface, I felt like my hands were tied in terms of resolving some of the issues I was seeing with the bwa toolbox. It seems I was right.
I will see what could be done in terms of gaining command-line access to the Galaxy directory. Thank you for your advice!
Ray
On Wed, Sep 23, 2015 at 12:12 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan rwan.work@gmail.com wrote:
Hi Peter,
On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
Hi Ray,
You will absolutely need command line access to the Galaxy server for some of the administration tasks - the web admin controls and web report tool only let you do some of the likely tasks.
During the initial setup admin (sudo) rights would be useful, at very least you'll need the sys admin to help with mounting shared network drives, cluster integration, database setup. If you want to run cluster jobs as the associated Unix account of each user, or anything like LDAP logins, then again you will need help from your sys admin.
I see!
Sorry to go off on a tangent, but something I'm marginally familiar with is content management systems (CMS) such as Joomla and WordPress and maybe I can use it as an analogy to make sure I understand. For those, suppose we create an account "ray" who owns or is in a group with the Apache process who owns:
- the directory that Joomla resides in and all subdirectories,
- is the database administrator of the MySQL database, and
- is the administrator of the Joomla web interface
then I wouldn't need sudo access. On occasion, the Apache configuration might need to be changed and the system administrator can be asked to do that, but that's probably once a year or something.
Is Galaxy like this? Or do you reckon I need full sudo access?
Sorry, I just want to make sure when I ask for greater access, I have an idea how Galaxy works or how it might differ from a CMS.
There are certainly similarities with the CMS idea - Galaxy also has its own user accounts, and interacts with Apache.
I would certainly opt for a galaxy Linux user account with minimal rights (no sudo!), which would own all the files by default, and also galaxy specific database accounts (probably PostgreSQL not MySQL).
We then install various Galaxy specific dependencies like samtools under $HOME/bin which is on the Galaxy user's $PATH - which like the main Tool Shed dependency mechanism installs tools locally without needing sys admin rights on the Galaxy server or cluster.
When I have needed sudo has been during Galaxy setup (often), but only occasionally since (e.g. debugging and needing to restart services, or changing Apache settings).
Peter