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 <tbo...@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 <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 > > > > > > ___________________________________________________________ > > > 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 <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 > > ___________________________________________________________ > 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/ >
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