[Bio-Linux] Bio-Linux 8 Repositories

Wed May 13 19:19:57 EDT 2015

Hi Tim,

Thank you for sharing this command:

wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | env
UNPACK_ONLY=1 sh

Now I can finally see what you are doing in file "upgrade_to_8.sh" to
transform Ubuntu 14.04 LTS into Biolinux 8.

I recently upgraded my system to Ubuntu 15.04 Wily Werewolf (Kernel
4.1rc2)  and even after that most of the packages from Biolinux 8
repositories are still working pretty well. I think there is a conflict
between the old mate packages from Biolinux in launchpad and the fresh new
mate packages from the official Ubuntu repositories. Keep up the good work!

Interesting to see the packages in pseudo_orphans.txt as well!

Here are a two bugs I'm receiving while running your script:

*This one, probably because of the change from upstart to systemd:*

initctl: Unable to connect to Upstart: Failed to connect to socket
/com/ubuntu/upstart: Connection refused
insserv: warning: script 'galaxy' missing LSB tags and overrides
insserv: Default-Start undefined, assuming empty start runlevel(s) for
script `galaxy'
insserv: Default-Stop  undefined, assuming empty stop  runlevel(s) for
script `galaxy'

*And this second one:*

E: Unable to locate package bio-linux-jalview
Not all packages installed properly - exiting.

I believe it's something related with the package "jalview" from biolinux
repo. I could install this package from Ubuntu sources without a problem:

 http://archive.ubuntu.com/ubuntu/ wily/universe jalview all 2.7.dfsg-4
[3.382 kB]

*Now I have a question, after changing the name of the package in file
"bl_master_package_list.txt" from **bio-linux-jalview to *
*jalview, how I could "pack" everything again to the file upgrade8.sh
<http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh> or in which order I
should execute your scripts bl_install_master_list.sh, pick_cran_mirror.py
and upgrade_to_8.sh in order to finally complete the upgrade to Biolinux 8
?*

I believe I could help this project by packaging some new software to add
to the biolinux repositories or even trying to upgrade a package from
python2 to python3.

Let me know how I could help. :)

Kind Regards,

_____________________________________________

Raony Guimarães Corrêa Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________

On Wed, May 13, 2015 at 11:24 AM, Simon <simon at calmblue.net> wrote:

> On 13/05/15 15:14, Tony Travis wrote:
>
>> On 13/05/15 15:01, Simon wrote:
>>
>>> Hi Tim, that's brilliant, thanks.
>>>
>>> Script looks good to me, although I think the PPA will be best for our
>>> situation as we're not running a GUI and the less we vary from our
>>> standard server build the better.
>>>
>> Hi, Simon.
>>
>> I've run Bio-Linux 8 as a terminal server on many servers. You need most
>> of the Ubuntu 'desktop' installed to run a remote MATE desktop.
>>
>> I don't think it's an issue to run a GUI on a server, but you might find
>> it useful to use the MATE desktop locally if the server graphics
>> hardware is not up to running Unity.
>>
>> The overhead of running a GUI on the server is quite low, especially if
>> you run the MATE desktop locally. The default remote desktop is MATE.
>>
>> HTH,
>>
>>    Tony.
>>
>>
> Good to know, thanks, I like MATE. If it turns out that a desktop is
> required then I'll definitely go down that route.
>
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>
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