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.c...@googlemail.com> wrote:
> On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan <rwan.w...@gmail.com> wrote:
>> Hi Peter,
>>
>>
>> On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock <p.j.a.c...@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:
>>
>> 1)  the directory that Joomla resides in and all subdirectories,
>> 2)  is the database administrator of the MySQL database, and
>> 3)  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
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