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

[William Spooner]

On 16 Jul 2012, at 17:57, Tim Booth wrote:

> Hi Will,
> 
>> 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
> 
> Ah yes, the version of python-rpy in our repository is compiled to work
> with the latest version of r-base-core from CRAN, and APT isn't smart
> enough (without hinting) to know that it needs to pick the version off
> the Ubuntu server rather then the NEBC server.
> 
> Two possible fixes for this:
> 
> 1) Get CRAN to make a working version of python-rpy so I don't need to
> roll my own
> 
> 2) Teach Galaxy to use python-rpy2 instead

Circular dependency hell? Don't envy you…

Will


> 
> I'll look into both of these.
> 
> Cheers,
> 
> TIM
> 
> -- 
> 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