[Bio-Linux] Bio-Linux 8 Repositories
Tim Booth
tbooth at ceh.ac.uk
Thu May 14 11:47:54 EDT 2015
Hi Raony,
The packing thing was never supposed to obfuscate the upgrade process,
just to make distribution easier for me. If you or anyone else on the
list would find the packer script useful it is here, along with some
other bits and pieces I wrote:
http://bazaar.launchpad.net/~tbooth/+junk/misc_scripts/files
(packit.perl is the script; testpack.sh is a test case for it)
But you don't need to repack anything, just cd to the temporary
directory and run "sudo upgrade_to_8.sh".
For MATE, you should definitely use the official Wily packages. When I
write the upgrade script for 16.04 I'll ensure it replaces my packages
with the mainstream ones.
Jalview was a bug - I'd changed the package name and didn't update the
script. I've fixed it in the same way you did.
Galaxy is not going to work on Wily without some significant work on my
part. As you said it needs converting to SystemD but I think it needs a
bit more than that in addition.
As for getting involved in the project, I'll answer that in a second
e-mail.
Cheers,
TIM
On Wed, 2015-05-13 at 20:19 -0300, Raony Guimaraes Corrêa Do Carmo
Lisboa Cardenas wrote:
> 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 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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--
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://environmentalomics.org/bio-linux
+44 1491 69 2297
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