[Bio-linux-dev] bio-linux-galaxy or galaxy-server

[William Spooner]

Hi Tim,

I'm rolling my own BioLinux by adding the repositories to sources.list. When installing galaxy on 10.04 I get the following;

---
$ sudo apt-get install galaxy-server-all
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  galaxy-server-all: Depends: python-rpy but it is not going to be installed
                     Recommends: ucsc-tools-non-free but it is not installable
                     Recommends: laj but it is not installable
E: Broken packages
---

The error is because galaxy needs a very specific version of python-rpy (due to a cascade to r-base-core) that I can get as follows;

$ sudo apt-get install python-rpy=1.0.3-17lucid1

galaxy-server-all now installs correctly.

Best,

will


On 9 Jul 2012, at 16:02, Tim Booth wrote:

> Hi Will,
> 
> Sorry, the redundant bio-linux-* packages have now been cleaned off the
> server.  All the packages (aside from the OpenOffice one which has
> nothing to do with this) are ours.  If you want to try Galaxy with all
> the default package dependencies, install "galaxy-server-all".
> 
> These have not yet been officially announced because, while complete,
> there is still a bit more testing to do before I'm happy and we can
> co-ordinate an announcement with our collaborators in Manchester.
> 
> Note that you'll get a warning about two missing packages - we can't put
> these on the main server due to licensing restrictions.
> 
> And yes, I'd be interested in the startup script.  I need to review the
> latest packaging guidelines but I think we'll need separate startup
> scripts for Ubuntu and Debian if this is to work on both.  There's some
> way to go before the Galaxy packages (at least the core) could make it
> to Debian-Med, though, as I've employed some very nasty hacks to get
> them building!
> 
> Cheers,
> 
> TIM
> 
>> $ aptitude search galaxy
>> p   bio-linux-galaxy-all  - A web-based analysis environment with third party dependencies                                
>> p   bio-linux-galaxy-core - A web-based analysis environment                                                              
>> p   bio-linux-galaxy-dependencies - Third party dependencies for Galaxy (a web-based analysis tool)                               
>> p   galaxy-server - A web-based analysis environment                                                              
>> p   galaxy-server-all - Galaxy server with all recommended tools                                                      
>> p   galaxy-server-test - Test and demo data for Galaxy server                                                          
>> p   openoffice.org-style-galaxy - office productivity suite -- Galaxy (Default) symbol style        
>> 
>> So galaxy seems to be packaged twice, once by bio-linux, and once
>> elsewhere. Tim and Soon Gweon are the maintainers in bot cases. So -
>> should I be using bio-linux-galaxy or galaxy-server?
>> 
>> Tim - I also have a debian service-compatible init.d startup script
>> for galaxy if you're interested. Similar to the
>> current /etc/init/galaxy.conf, but with greater functionality.
>> 
>> Best,
>> 
>> Will
>> 
>> ---
>> William Spooner           http://eaglegenomics.com
>> M:07779-663045 E:william.spooner at eaglegenomics.com 
>> 
>> _______________________________________________
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>> Bio-Linux-dev at nebclists.nerc.ac.uk
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> 
> -- 
> Tim Booth <tbooth at 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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---
William Spooner           http://eaglegenomics.com
M:07779-663045 E:william.spooner at eaglegenomics.com