[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)

[Tony Travis]

On 26/09/12 17:52, Tony Travis wrote:
> On 26/09/12 17:45, Tony Travis wrote:
>> [...]
>> I'll look into it and see if I can come up with a fix.

Hi, Tim.

I downloaded your script:

> wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh

I edited "bio-linux-qiime" out of the list, then ran it locally:

> chmod +x bl_master_package_list.sh
> ./bl_master_package_list.sh
> [...]
> E: Unable to locate package estscan2

This is because the adding the PPA failed:

> ./bl_do_update_to7.sh: line 55: apt-add-repository: command not found
> ./bl_do_update_to7.sh: line 58: apt-add-repository: command not found

This, which I didn't notice first time round, I fixed by:

   aptitude install python-software-properties

I modified your installer to run the script without Qiime locally:

> root at bifx-rta:/usr/local/src/NEBC/Bio-Linux-upgrade# diff bl_do_update_to7.sh bl_do_update_to7.sh.orig
> 138,139c138
> < #runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh"
> < ./bl_master_package_list.sh
> ---
>> runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh"

And I got:

All done - your system is updated to Bio-Linux 7!

Thanks for all your work creating this Bio-Linux 7 update script.

Bye,

   Tony.