Hi,

This is mainly a message to Carlos and Eric who volunteered to get
involved with my Debian packaging, but of course any other help will
also be appreciated.  If either of you can spare time now it is a good
moment to do so.

I've been working on my package stuff over the last couple of weeks and
have uploaded the latest to Debian-Med ready to build:

http://anonscm.debian.org/viewvc/debian-med/trunk/packages/galaxy/trunk/debian/?view=log

Note that you need the re-packed tarball as generated by
get-orig-source.sh and if you have a problem generating that you can
grab a copy of it here:

https://launchpad.net/~nebc/+archive/galaxy/+files/galaxy_1.bl.py27.20140210.orig.tar.xz

I've only built this for Ubuntu, and I know that to get it working on
Debian you'll at least need to replace the upstart job with
an /etc/init.d script.  After that I think you should have something
working (see my commit notes).

My latest efforts have been to try and get tool-shed installs working.
Galaxy expects to be able to write to its own shed_tools_*_conf.xml
files as well as to shed_tools and the tool-data directory.  It looks
like there is work to have a separate shed_tool-data folder but this is
not fully working so I'm seeing if I can patch it.  Either way, it's
vital for packaging that the files managed by DPKG and the files
(over)written by the Galaxy server are separated out into /var and /usr
respectively.

Cheers,

TIM

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?).
>
> 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...
>
> Thanks for your work on this,
> Carlos
>
>
> On Fri, Dec 13, 2013 at 7:03 AM, Tim Booth <tbooth@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 <tbooth@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
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
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> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/

--
Tim Booth <tbooth@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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/