Hi John and Carlos,
Thanks for your replies regarding my DEB packaging work. Some quick
answers to questions you raised.
> In response to the eggs comment in the changelog - there are upsides
> and downsides to the way Galaxy handles dependency fetching but I
> think there should at least be an off switch. I thought that would be
> easy, but it sounds like not:
> I have created a Trello card for this.
Of course the ultimate goal for Debian compliance is that Galaxy uses
100% system Python libs and DPKG looks after all the interdependencies.
I'm not sure how realistic that is, but I'm working on it. I'll need
good regression tests for sure.
On Mon, 2013-12-16 at 16:27 +0000, Carlos Borroto wrote:
> Hi Tim,
> This sounds great. I'll be happy to help testing and hopefully find
> some time to help packaging once it gets into Debian Med(are you
> submitting all your packages there?).
Yes, it will all go in the Debian-Med SVN but for it to actually work on
Debian I'll need a non-Upstart init script and probably some other
changes. Maybe you can help me with that? I'll ping you in the New
> One question, for apache/nginx configuration why not use something ala
> phpMyAdmin which ask you if you want to preconfigure the package with
> a webserver in particular. The name of the DEB packaging technology to
> ask these kind of questions is evading me now. I think using something
> like that could open many possibilities in the future, like database
> backend to use, home URL, admin user/password, etc...
I think you mean Debconf, which I'll probably use for a couple of things
like the initial list of admin users but which I try to limit. If I put
the packages out on the live DVD/USB or the Cloud image then I have to
configure them with default settings in any case, and then it's easier
for the user to just edit the config files than to remember a command
% sudo dpkg-reconfigure -p medium galaxy-server-apache-proxy
As a case in point, the apache2 package itself no longer uses debconf at
I'm not currently planning to add Nginx to this packaging, as the
priority was to enable uploads via SFTP, and this required use of system
accounts in Galaxy, which called for authentication via PAM, which
needed the relevant Apache2 modules.
> Thanks for your work on this,
> On Fri, Dec 13, 2013 at 7:03 AM, Tim Booth <tbo...@ceh.ac.uk> wrote:
> > Hi All,
> > As previously mentioned, I'm back working on packaging the Galaxy server
> > as DEB packages for Bio-Linux (ie. Ubuntu 12.04 LTS) and ultimately
> > pushing towards something that could be Debian compliant. There's a way
> > to go in that regard, but I do now have an updated package for Bio-Linux
> > in final testing and it also has a new trick: doing "apt-get install
> > galaxy-server-apache-proxy" will set up just that with no further
> > configuration needed. The galaxy server appears at
> > http://localhost/galaxy and users log in with their regular system
> > username and password. Uploads are enabled via regular SFTP so no
> > special FTP server configuration is needed.
> > It's a little hacky in parts but I'm generally pleased with the result.
> > If anyone want to take a look I'd welcome comments. It's not in the
> > main BL repo yet but can be found here:
> > https://launchpad.net/~nebc/+archive/galaxy/+sourcepub/3711751/+listing-archive-extra
> > Cheers,
> > TIM
> > --
> > Tim Booth <tbo...@ceh.ac.uk>
> > NERC Environmental Bioinformatics Centre
> > Centre for Ecology and Hydrology
> > Maclean Bldg, Benson Lane
> > Crowmarsh Gifford
> > Wallingford, England
> > OX10 8BB
> > http://nebc.nerc.ac.uk
> > +44 1491 69 2705
> > ___________________________________________________________
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Tim Booth <tbo...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
+44 1491 69 2705
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