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

[Tim Booth]

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

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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