Hi Nate,
It's great to hear that my rearrangements for packaging Galaxy are
somewhat in line with what you are doing. My package is a bit of a
rats-nest of symlinks right now but I'll clean these up as things become
more configurable.
One thing I'm a bit stuck on is the tool_data_table_conf.xml and
shed_tool_data_table_conf.xml files. If the former is installed and
updated by my package and the latter is managed by the internal
tool-shed logic then this leaves nowhere for the user to make manual
edits (we can use the debian config-files system to share ownership but
it's awkward). Also I've made a galaxy-tools-bl package that adds some
standard tool definitions in a file called bl_tool_conf.xml. I can set
things up so this is seen by Galaxy:
[app:main]
...
tool_config_file = tool_conf.xml,shed_tool_conf.xml,bl_tool_conf.xml
So I can split out tool_conf.xml but currently I can't split out items
in tool_data_table_conf.xml (unless I make a startup script that
compiles it on the fly from XML fragments, in the style of
build_universe_config.py). Now if it were me I'd try and eliminate this
XML file altogether, and have Galaxy just collect up all the
available .loc files on startup without the need for a central registry
file. This would involve embedding the couple of bits of metadata from
the tool_data_table_conf.xml XML file into the .loc files themselves,
and maybe there is some reason I've not spotted why this would be a bad
idea. Any thoughts on this? Is it something you have considered or
would consider?
Cheers,
TIM
On Fri, 2014-03-28 at 18:49 +0000, Nate Coraor wrote:
> Hi Tim,
>
>
> I have recently been working on getting Galaxy Main's configs and
> server-modified files and directories out of the galaxy-dist
> directory, so our goals are aligning. Not everything can be moved
> without some trickery (e.g. symlinks) but most paths, including the
> paths to shed_*.xml are configurable in universe_wsgi.ini (which
> itself need not live in the galaxy-dist directory).
>
>
> --nate
>
>
> On Mon, Mar 24, 2014 at 1:38 PM, Tim Booth <tbooth@ceh.ac.uk> wrote:
> 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
> > > 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/
>
> --
> 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/
>
>
>
--
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