From dbradshaw3366 at gmail.com  Fri Aug 12 16:00:50 2016
From: dbradshaw3366 at gmail.com (David Bradshaw)
Date: Fri, 12 Aug 2016 16:00:50 -0400
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
	problems with qiime
Message-ID: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>

Dear Whom It May Concern,

I may have accidentally sent this email to the wrong place initially, I
apologize. I upgraded to Ubuntu 16.04 and now there are items within qiime
that are not working. I imagine I may have removed some essential items
during the upgrade? What would be the best way to fix this? Below are some
of the errors I am encountering with the print_qiime_config_all and
join_paired_ends commands.

Thank you for your time and help,

Sincerely,

David Bradshaw


microbiology at microbiology-OptiPlex-9020[microbiology] qiime           [
1:35PM]
join_paired_ends.py
Setting up ZSH (/bin/zsh) environment to run QIIME commands.

You have QIIME version UNKNOWN.
Note that this will not produce identical results to the official QIIME
release
as it uses updated versions of several tools.

Type 'help' for help, 'print_qiime_config_all' to see the current QIIME
settings, or 'exit' to return to regular shell.

microbiology at microbiology-OptiPlex-9020[microbiology]  qiime >
print_qiime_config_all
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This may
take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This
may take a moment.')
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 57, in <module>
    raise ImportError("%s\n%s" % (e, core_dependency_missing_msg))
ImportError: cannot import name OrdinationResults
See the QIIME Installation Guide: http://qiime.org/install/install.html

Here are the versions of the packages that QIIME depends on as reported by
the system package manager:

ampliconnoise             : 1.29-5build1
blast2                    : 1:2.2.26.20120620-10
bwa                       : 0.7.12-5
cd-hit                    : 4.6.4-1
chimeraslayer             : 20101212+dfsg1-1
clearcut                  : 1.0.9-1
clustalw                  : 2.1+lgpl-4
ea-utils                  : 1.1.2+dfsg-3
emperor                   : 0.9.51-0biolinux1
fasttree                  : 2.1.8-2
infernal                  : 1.1.1-3
mafft                     : 7.271-1
mothur                    : 1.36.1-1build1
muscle                    : 1:3.8.31+dfsg-1
parsinsert                : 1.04-1biolinux1.1
pynast                    : 1.2.2-1
python                    : 2.7.11-1
python-biom-format        : 2.1.5+dfsg-1
python-burrito            : 0.9.1-1
python-burrito-fillings   : 0.1.0-0biolinux4
python-cogent             : 1.5.3-10
python-matplotlib         : 1.5.1-1ubuntu1
python-mpi4py             : 1.3.1+hg20131106-2ubuntu5
python-numpy              : 1:1.11.0-1ubuntu1
python-pandas             : 0.17.1-3ubuntu2
python-qcli               : 0.1.0-1
python                    : 2.7.11-1
qiime-data                : 1.9.0+dfsg-0biolinux5
qiime-default-reference   : 0.1.1-0biolinux2
r-cran-optparse           : 1.3.0-1cran1ppa0
raxml                     : 8.2.4-1
rdp-classifier            : 2.10.2-1
seqprep                   : 1.1-4ubuntu1
sortmerna                 : 2.0-1
sumatra                   : 1.0.10-1
swarm                     : 2.1.6-1
vsearch                   : 1.1.3+dfsg-1

OK
microbiology at microbiology-OptiPlex-9020[microbiology]  qiime >
join_paired_ends.py -f DCH2_062216/4653_C1S616-515wF-806bR_R1.fastq -r
DCH2_062216/4653_C1S616-515wF-806bR_R2.fastq -o C1S616
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This may
take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This
may take a moment.')
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/join_paired_ends.py", line 11, in <module>
    from qiime.join_paired_ends import (join_method_names,
  File "/usr/lib/python2.7/dist-packages/qiime/join_paired_ends.py", line
11, in <module>
    from skbio.parse.sequences import parse_fastq
ImportError: No module named parse.sequences
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From tony.travis at minke-informatics.co.uk  Sat Aug 13 12:20:29 2016
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sat, 13 Aug 2016 17:20:29 +0100
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
Message-ID: <24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>

On 12/08/16 21:00, David Bradshaw wrote:
> Dear Whom It May Concern,
> 
> I may have accidentally sent this email to the wrong place initially, I
> apologize. I upgraded to Ubuntu 16.04 and now there are items within
> qiime that are not working. I imagine I may have removed some essential
> items during the upgrade? What would be the best way to fix this? Below
> are some of the errors I am encountering with the print_qiime_config_all
> and join_paired_ends commands.

Hi, David.

I've also upgraded Bio-Linux 8 on my laptop "beluga" to Ubuntu 16.04 LTS
and there are a few problems: I've confirmed your bug report, which is
caused by the "xenial" (16.04) version of python-skbio taking
prece4dence over Tim's Bio-Linux version:

> root at beluga:~# apt-cache policy python-skbio
> python-skbio-doc:
>   Installed: (none)
>   Candidate: 0.4.1-1
>   Version table:
>      0.4.1-1 500
>         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
>         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe i386 Packages
> python-skbio:
>   Installed: 0.4.1-1
>   Candidate: 0.4.1-1
>   Version table:
>  *** 0.4.1-1 500
>         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
>         100 /var/lib/dpkg/status
>      0.2.3-0biolinux2 500
>         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64 Packages

Force the version to make "apt" downgrade to the Bio-Linux 8 version:

> root at beluga:~# apt install python-skbio=0.2.3-0biolinux2
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> The following packages were automatically installed and are no longer required:
>   python-bz2file python-cachecontrol python-contextlib2 python-requests
> Use 'sudo apt autoremove' to remove them.
> The following packages will be DOWNGRADED:
>   python-skbio
> 0 to upgrade, 0 to newly install, 1 to downgrade, 0 to remove and 0 not to upgrade.
> Need to get 257 kB of archives.
> After this operation, 1,953 kB disk space will be freed.
> Do you want to continue? [Y/n] 
> Get:1 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64 python-skbio amd64 0.2.3-0biolinux2 [257 kB]
> Fetched 257 kB in 0s (715 kB/s)      
> dpkg: warning: downgrading python-skbio from 0.4.1-1 to 0.2.3-0biolinux2
> (Reading database ... 522743 files and directories currently installed.)
> Preparing to unpack .../python-skbio_0.2.3-0biolinux2_amd64.deb ...
> Unpacking python-skbio (0.2.3-0biolinux2) over (0.4.1-1) ...
> Setting up python-skbio (0.2.3-0biolinux2) ...
> root at beluga:~# apt-cache policy python-skbio
> python-skbio:
>   Installed: 0.2.3-0biolinux2
>   Candidate: 0.4.1-1
>   Version table:
>      0.4.1-1 500
>         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
>  *** 0.2.3-0biolinux2 500
>         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64 Packages
>         100 /var/lib/dpkg/status
> 

There are still many problems with the OpenMPI support for QIIME, but at
least this is a step in the right direction :-)

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

From dbradshaw3366 at gmail.com  Sat Aug 13 12:24:34 2016
From: dbradshaw3366 at gmail.com (David Bradshaw)
Date: Sat, 13 Aug 2016 12:24:34 -0400
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
	<24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
Message-ID: <CAG0VSgoF4B=JVjwkNa5LCge_VZLWkp0FM08DJx6iFJXmqj71qw@mail.gmail.com>

Dear Tony Travis,

Thank you very much. I will try doing that once I get back to my computer.
Thank you again very much.

Sincerely,

David Bradshaw

On Aug 13, 2016 12:20 PM, "Tony Travis" <tony.travis at minke-informatics.co.uk>
wrote:

> On 12/08/16 21:00, David Bradshaw wrote:
> > Dear Whom It May Concern,
> >
> > I may have accidentally sent this email to the wrong place initially, I
> > apologize. I upgraded to Ubuntu 16.04 and now there are items within
> > qiime that are not working. I imagine I may have removed some essential
> > items during the upgrade? What would be the best way to fix this? Below
> > are some of the errors I am encountering with the print_qiime_config_all
> > and join_paired_ends commands.
>
> Hi, David.
>
> I've also upgraded Bio-Linux 8 on my laptop "beluga" to Ubuntu 16.04 LTS
> and there are a few problems: I've confirmed your bug report, which is
> caused by the "xenial" (16.04) version of python-skbio taking
> prece4dence over Tim's Bio-Linux version:
>
> > root at beluga:~# apt-cache policy python-skbio
> > python-skbio-doc:
> >   Installed: (none)
> >   Candidate: 0.4.1-1
> >   Version table:
> >      0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe i386
> Packages
> > python-skbio:
> >   Installed: 0.4.1-1
> >   Candidate: 0.4.1-1
> >   Version table:
> >  *** 0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >         100 /var/lib/dpkg/status
> >      0.2.3-0biolinux2 500
> >         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main
> amd64 Packages
>
> Force the version to make "apt" downgrade to the Bio-Linux 8 version:
>
> > root at beluga:~# apt install python-skbio=0.2.3-0biolinux2
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > The following packages were automatically installed and are no longer
> required:
> >   python-bz2file python-cachecontrol python-contextlib2 python-requests
> > Use 'sudo apt autoremove' to remove them.
> > The following packages will be DOWNGRADED:
> >   python-skbio
> > 0 to upgrade, 0 to newly install, 1 to downgrade, 0 to remove and 0 not
> to upgrade.
> > Need to get 257 kB of archives.
> > After this operation, 1,953 kB disk space will be freed.
> > Do you want to continue? [Y/n]
> > Get:1 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64
> python-skbio amd64 0.2.3-0biolinux2 [257 kB]
> > Fetched 257 kB in 0s (715 kB/s)
> > dpkg: warning: downgrading python-skbio from 0.4.1-1 to 0.2.3-0biolinux2
> > (Reading database ... 522743 files and directories currently installed.)
> > Preparing to unpack .../python-skbio_0.2.3-0biolinux2_amd64.deb ...
> > Unpacking python-skbio (0.2.3-0biolinux2) over (0.4.1-1) ...
> > Setting up python-skbio (0.2.3-0biolinux2) ...
> > root at beluga:~# apt-cache policy python-skbio
> > python-skbio:
> >   Installed: 0.2.3-0biolinux2
> >   Candidate: 0.4.1-1
> >   Version table:
> >      0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >  *** 0.2.3-0biolinux2 500
> >         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main
> amd64 Packages
> >         100 /var/lib/dpkg/status
> >
>
> There are still many problems with the OpenMPI support for QIIME, but at
> least this is a step in the right direction :-)
>
> 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
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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From dbradshaw2015 at fau.edu  Mon Aug 15 10:15:09 2016
From: dbradshaw2015 at fau.edu (David Bradshaw)
Date: Mon, 15 Aug 2016 10:15:09 -0400
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
	<24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
Message-ID: <CAK5-mLYSFMdxFG-jfPjxX2Lc4LbPzO+DbZ1+4kKi_HQ2p6dLPA@mail.gmail.com>

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?

microbiology at microbiology-OptiPlex-9020[microbiology] sudo 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] sudo apt install
python-skbio=0.2.3-0biolinux2
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Version '0.2.3-0biolinux2' for 'python-skbio' was not found
microbiology at microbiology-OptiPlex-9020[microbiology]
[10:12AM]

Thank you for your time and help,

Sincerely,

David Bradshaw

On Sat, Aug 13, 2016 at 12:20 PM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 12/08/16 21:00, David Bradshaw wrote:
> > Dear Whom It May Concern,
> >
> > I may have accidentally sent this email to the wrong place initially, I
> > apologize. I upgraded to Ubuntu 16.04 and now there are items within
> > qiime that are not working. I imagine I may have removed some essential
> > items during the upgrade? What would be the best way to fix this? Below
> > are some of the errors I am encountering with the print_qiime_config_all
> > and join_paired_ends commands.
>
> Hi, David.
>
> I've also upgraded Bio-Linux 8 on my laptop "beluga" to Ubuntu 16.04 LTS
> and there are a few problems: I've confirmed your bug report, which is
> caused by the "xenial" (16.04) version of python-skbio taking
> prece4dence over Tim's Bio-Linux version:
>
> > root at beluga:~# apt-cache policy python-skbio
> > python-skbio-doc:
> >   Installed: (none)
> >   Candidate: 0.4.1-1
> >   Version table:
> >      0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe i386
> Packages
> > python-skbio:
> >   Installed: 0.4.1-1
> >   Candidate: 0.4.1-1
> >   Version table:
> >  *** 0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >         100 /var/lib/dpkg/status
> >      0.2.3-0biolinux2 500
> >         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main
> amd64 Packages
>
> Force the version to make "apt" downgrade to the Bio-Linux 8 version:
>
> > root at beluga:~# apt install python-skbio=0.2.3-0biolinux2
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > The following packages were automatically installed and are no longer
> required:
> >   python-bz2file python-cachecontrol python-contextlib2 python-requests
> > Use 'sudo apt autoremove' to remove them.
> > The following packages will be DOWNGRADED:
> >   python-skbio
> > 0 to upgrade, 0 to newly install, 1 to downgrade, 0 to remove and 0 not
> to upgrade.
> > Need to get 257 kB of archives.
> > After this operation, 1,953 kB disk space will be freed.
> > Do you want to continue? [Y/n]
> > Get:1 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64
> python-skbio amd64 0.2.3-0biolinux2 [257 kB]
> > Fetched 257 kB in 0s (715 kB/s)
> > dpkg: warning: downgrading python-skbio from 0.4.1-1 to 0.2.3-0biolinux2
> > (Reading database ... 522743 files and directories currently installed.)
> > Preparing to unpack .../python-skbio_0.2.3-0biolinux2_amd64.deb ...
> > Unpacking python-skbio (0.2.3-0biolinux2) over (0.4.1-1) ...
> > Setting up python-skbio (0.2.3-0biolinux2) ...
> > root at beluga:~# apt-cache policy python-skbio
> > python-skbio:
> >   Installed: 0.2.3-0biolinux2
> >   Candidate: 0.4.1-1
> >   Version table:
> >      0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >  *** 0.2.3-0biolinux2 500
> >         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main
> amd64 Packages
> >         100 /var/lib/dpkg/status
> >
>
> There are still many problems with the OpenMPI support for QIIME, but at
> least this is a step in the right direction :-)
>
> 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
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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From tony.travis at minke-informatics.co.uk  Tue Aug 16 18:27:01 2016
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 16 Aug 2016 23:27:01 +0100
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <CAK5-mLYSFMdxFG-jfPjxX2Lc4LbPzO+DbZ1+4kKi_HQ2p6dLPA@mail.gmail.com>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
	<24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
	<CAK5-mLYSFMdxFG-jfPjxX2Lc4LbPzO+DbZ1+4kKi_HQ2p6dLPA@mail.gmail.com>
Message-ID: <bcacc805-7a73-02f0-1e6a-a9d106649feb@minke-informatics.co.uk>

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

From dbradshaw3366 at gmail.com  Tue Aug 16 19:46:49 2016
From: dbradshaw3366 at gmail.com (David Bradshaw)
Date: Tue, 16 Aug 2016 19:46:49 -0400
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <CAG0VSgrTfFKOiu_5RziD78hARX7Y2V4_guN0Wbk9-VVDCLOw8g@mail.gmail.com>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
	<24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
	<CAK5-mLYSFMdxFG-jfPjxX2Lc4LbPzO+DbZ1+4kKi_HQ2p6dLPA@mail.gmail.com>
	<bcacc805-7a73-02f0-1e6a-a9d106649feb@minke-informatics.co.uk>
	<CAG0VSgrTfFKOiu_5RziD78hARX7Y2V4_guN0Wbk9-VVDCLOw8g@mail.gmail.com>
Message-ID: <CAG0VSgquRgqx_xNF-_PF_S1JBnhFdz8vd4SAYhyhzXq71nbckg@mail.gmail.com>

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
>> _______________________________________________
>> Bio-Linux-list mailing list
>> Bio-Linux-list at bioinformatics.org
>> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>>
>
>
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From tony.travis at minke-informatics.co.uk  Tue Aug 16 20:05:44 2016
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Wed, 17 Aug 2016 01:05:44 +0100
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <CAG0VSgquRgqx_xNF-_PF_S1JBnhFdz8vd4SAYhyhzXq71nbckg@mail.gmail.com>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
	<24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
	<CAK5-mLYSFMdxFG-jfPjxX2Lc4LbPzO+DbZ1+4kKi_HQ2p6dLPA@mail.gmail.com>
	<bcacc805-7a73-02f0-1e6a-a9d106649feb@minke-informatics.co.uk>
	<CAG0VSgrTfFKOiu_5RziD78hARX7Y2V4_guN0Wbk9-VVDCLOw8g@mail.gmail.com>
	<CAG0VSgquRgqx_xNF-_PF_S1JBnhFdz8vd4SAYhyhzXq71nbckg@mail.gmail.com>
Message-ID: <f7e0814d-cb3f-b7a8-30e4-c4fcab84cc1e@minke-informatics.co.uk>

On 17/08/16 00:46, David Bradshaw wrote:
> 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.

Hi, David.

You have to update APT after editing any repository source config:

  apt update

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

From dbradshaw3366 at gmail.com  Tue Aug 16 20:18:34 2016
From: dbradshaw3366 at gmail.com (David Bradshaw)
Date: Tue, 16 Aug 2016 20:18:34 -0400
Subject: [Bio-linux-list] Updated to Ubuntu 16.04 and now I am having
 problems with qiime
In-Reply-To: <f7e0814d-cb3f-b7a8-30e4-c4fcab84cc1e@minke-informatics.co.uk>
References: <CAG0VSgov-V2Dm+vTGmYbRbpxV9Fk0cCwpsaQ1YKUQ+=oGPwimQ@mail.gmail.com>
	<24c47450-5af9-0bb9-6884-b29fd5f5ff49@minke-informatics.co.uk>
	<CAK5-mLYSFMdxFG-jfPjxX2Lc4LbPzO+DbZ1+4kKi_HQ2p6dLPA@mail.gmail.com>
	<bcacc805-7a73-02f0-1e6a-a9d106649feb@minke-informatics.co.uk>
	<CAG0VSgrTfFKOiu_5RziD78hARX7Y2V4_guN0Wbk9-VVDCLOw8g@mail.gmail.com>
	<CAG0VSgquRgqx_xNF-_PF_S1JBnhFdz8vd4SAYhyhzXq71nbckg@mail.gmail.com>
	<f7e0814d-cb3f-b7a8-30e4-c4fcab84cc1e@minke-informatics.co.uk>
Message-ID: <CAG0VSgq3o0qnEtVvOHDzctN_mi86ZQcRowbpSW+GLOb65=QBTA@mail.gmail.com>

Dear Tony Travis,

Thank you very much!! It seems like QIIME is working now.

Sincerely,

David Bradshaw

On Tue, Aug 16, 2016 at 8:05 PM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 17/08/16 00:46, David Bradshaw wrote:
> > 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.
>
> Hi, David.
>
> You have to update APT after editing any repository source config:
>
>   apt update
>
> 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
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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