[Bio-linux-list] Updated to Ubuntu 16.04 and now I am having problems with qiime

[David Bradshaw]

Dear Tony Travis,

Sorry, I was able to edit the file using the following script but, it is
still unable to find the biolinux version of skbio. Are there other files
that I need to edit? Thank you for your time and help.

Sincerely,

David Bradshaw

microbiology at microbiology-OptiPlex-9020[microbiology] gksudo gedit
/etc/apt/sources.list.d/nebc-bio-linux-trusty.list

** (gedit:25581): WARNING **: Set document metadata failed: Setting
attribute metadata::gedit-spell-enabled not supported

** (gedit:25581): WARNING **: Set document metadata failed: Setting
attribute metadata::gedit-encoding not supported

** (gedit:25581): WARNING **: Set document metadata failed: Setting
attribute metadata::gedit-position not supported

microbiology at microbiology-OptiPlex-9020[microbiology] apt-cache policy
python-skbio
python-skbio:
  Installed: 0.4.1-1
  Candidate: 0.4.1-1
  Version table:
 *** 0.4.1-1 500
        500 http://us.archive.ubuntu.com/ubuntu xenial/universe amd64
Packages
        100 /var/lib/dpkg/status

microbiology at microbiology-OptiPlex-9020[microbiology] cat
/etc/apt/sources.list.d/nebc-bio-linux-trusty.list
deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main # disabled
on upgrade to xenial
deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main #
disabled on upgrade to xenial

microbiology at microbiology-OptiPlex-9020[microbiology] sudo apt install
python-skbio=0.2.3-obiolinux2
[sudo] password for microbiology:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Version '0.2.3-obiolinux2' for 'python-skbio' was not found
microbiology at microbiology-OptiPlex-9020[microbiology]


On Tue, Aug 16, 2016 at 6:40 PM, David Bradshaw <dbradshaw3366 at gmail.com>
wrote:

> Dear Tony Travis,
>
> Thank you for the help. I tried to go to the /etc/apt/sources.list.d/nebc-bio-linux-trusty.list
> location and remove the # from the lines but it would not let me save the
> changes. Picture below. Thank you for your time and help, sorry that I keep
> having to ask for more help.
>
> Sincerely,
>
> David Bradshaw
>
> On Tue, Aug 16, 2016 at 6:27 PM, Tony Travis <tony.travis at minke-
> informatics.co.uk> wrote:
>
>> On 15/08/16 15:15, David Bradshaw wrote:
>> > Dear Tony Travis,
>> >
>> > I tried following your script above but it does not seem to recognize
>> > that the biolinux version exists. Please see below. Sorry, I am still a
>> > bit new to the qiime and linux systems. What would be the next step?
>>
>> Hi, David.
>>
>> You have to re-enable the Bio-Linux 8 PPA after upgrading:
>>
>> > root at beluga:~# cat /etc/apt/sources.list.d/nebc-bio-linux-trusty.list
>> > deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main #
>> disabled on upgrade to xenial
>> > deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main #
>> disabled on upgrade to xenial
>>
>> Uncomment the "#deb..." lines that the upgrade script commented out.
>>
>> HTH,
>>
>>   Tony.
>>
>> --
>> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
>> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
>> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
>> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
>> _______________________________________________
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>>
>
>
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