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 <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/ > > > -- 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/
