From paumarc at gmail.com  Wed Jan 13 07:48:30 2016
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Wed, 13 Jan 2016 13:48:30 +0100
Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics
In-Reply-To: <CANj1AG3s4=iKx=_5awzZM8fyc2sxYDXEi4LRJZN9cZYYTP+Q-g@mail.gmail.com>
References: <1450192871.23350.116.camel@balisaur>
	<CANj1AG3s4=iKx=_5awzZM8fyc2sxYDXEi4LRJZN9cZYYTP+Q-g@mail.gmail.com>
Message-ID: <CADFuJLgU+3rR+rkWEkPwL0RwbMftmM8sXT-c+jPyGMGU7P6gXA@mail.gmail.com>

maybe i am late,

 but good luck Tim and long live to biolinux!

:)

happy new year

p

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/


2015-12-30 1:36 GMT+01:00 Bishwa Kiran <kirannbishwa01 at gmail.com>:

> Hi Tim,
>
> Good luck on your new job. Thanks for the help you have been !!!
>
> Happy new year,
>
> On Tue, Dec 15, 2015 at 10:21 AM, Tim Booth <avarus at fastmail.fm> wrote:
>
>> Dear Bio-Linux users,
>>
>> For those who don't already know, I'm moving from my current job here in
>> the Thames Valley to the fair city of Edinburgh, specifically to work
>> for Edinburgh Genomics (https://genomics.ed.ac.uk/).
>>
>> In preparation I've been tidying up some things at this end and for
>> example you'll have seen today the relocation of the mailing lists, and
>> also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more.
>> The main website for Bio-Linux will remain at
>> http://environmentalomics.org/bio-linux.
>>
>> In terms of the future development of Bio-Linux and the prospective
>> Bio-Linux 9 I can't make any firm promises just yet but watch this
>> space.  If you want to get directly involved, join the -devel list
>> (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The
>> Ubuntu distribution and the Debian Med team, which provide 99% of
>> Bio-Linux functionality, are still going strong, but I still see a need
>> for a pre-configured bioinformatics distro and especially a platform to
>> support teaching and e-learning.  Therefore I'll do whatever I can
>> within my new job to stay involved with and promote the Bio-Linux
>> project.
>>
>> All the best, and Happy Christmas.
>>
>> TIM
>>
>> --
>> Hanlon's Razor: Never attribute to malice that which can be adequately
>> explained by stupidity... but don't rule out malice.
>>
>> _______________________________________________
>> Bio-Linux-list mailing list
>> Bio-Linux-list at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bio-linux-list
>>
>
>
>
> --
> - Bish
>
>
>
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bio-linux-list
>
>
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From kissaj at miamioh.edu  Wed Jan 20 13:01:20 2016
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Wed, 20 Jan 2016 13:01:20 -0500
Subject: [Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?
Message-ID: <1453312880.3248.9.camel@miamioh.edu>

Hello,

	Does anyone know the future plans for Bio-Linux?  In terms of
Bio-Linux 9 & Ubuntu 16.04 LTS?

Thanks,

-- 
 __________________________________________________________________
Andor J Kiss, Supervisor
Center for Bioinformatics and Functional Genomics
086 Pearson Hall ~ Miami University
700 East High Street
Oxford, Ohio? 45056
USA

eMAIL: kissaj at MiamiOH.edu 
Telephone: +1 (513) 529-4280
Fax: +1 (513) 529-2431
URL (CBFG): http://miamioh.edu/cas/academics/centers/cbfg/
URL (CBFG Services): https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics
URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss
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From kirannbishwa01 at gmail.com  Wed Jan 20 13:27:49 2016
From: kirannbishwa01 at gmail.com (Bishwa Kiran)
Date: Wed, 20 Jan 2016 13:27:49 -0500
Subject: [Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?
In-Reply-To: <1453312880.3248.9.camel@miamioh.edu>
References: <1453312880.3248.9.camel@miamioh.edu>
Message-ID: <CANj1AG34oNTvuYu4Q_H62a38vU0aDNDR3p2q12sYi-rymkNGRA@mail.gmail.com>

IDK, but I would very much like to keep up with updates regarding biolinux
and the ubuntu platform its built on.

(:

On Wed, Jan 20, 2016 at 1:01 PM, Andor J Kiss <kissaj at miamioh.edu> wrote:

> Hello,
>
> Does anyone know the future plans for Bio-Linux?  In terms of Bio-Linux 9
> & Ubuntu 16.04 LTS?
>
> Thanks,
> --
> __________________________________________________________________
> Andor J Kiss, Supervisor
> Center for Bioinformatics and Functional Genomics
> 086 Pearson Hall ~ Miami University
> 700 East High Street
> Oxford, Ohio  45056
> USA
>
> eMAIL: kissaj at MiamiOH.edu <kissaj at muohio.edu>
> Telephone: +1 (513) 529-4280
> Fax: +1 (513) 529-2431
> URL (CBFG): http://miamioh.edu/cas/academics/centers/cbfg/
> URL (CBFG Services):
> https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics
> URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss
>
>
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bio-linux-list
>
>


-- 
- Bish
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From tony.travis at minke-informatics.co.uk  Wed Jan 20 17:55:01 2016
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Wed, 20 Jan 2016 22:55:01 +0000
Subject: [Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?
In-Reply-To: <1453312880.3248.9.camel@miamioh.edu>
References: <1453312880.3248.9.camel@miamioh.edu>
Message-ID: <56A01045.6070203@minke-informatics.co.uk>

On 20/01/16 18:01, Andor J Kiss wrote:
> Hello,
> 
> Does anyone know the future plans for Bio-Linux?  In terms of Bio-Linux
> 9 & Ubuntu 16.04 LTS?

Hi, Andor.

I've already volunteered to help keep the Bio-Linux project rolling, but
it is unclear what, if any, continuation of EOS/NEBC funding there might
be to continue supporting Bio-Linux development.

I think we should let Tim Booth lead the discussion about Bio-Linux 9
when he has settled into his new job in Edinburgh.

Meanwhile, we in the Bio-Linux community can continue to provide help
and support for people who want to use the existing Bio-Linux 8.

I've had good success using Tim's 'upgrade' script to create physical
and virtual Bio-Linux instances based on 'standard' Ubuntu 14.04 LTS:

> http://environmentalomics.org/bio-linux-installation/
> wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh

There are some minor problems with the script, but one show-stopper is
the way Tim's script checks if you have the 'multiverse' repository
enabled in Ubuntu 14.04 LTS. This is how I did it under OpenStack on
iPlant Atmosphere recently:

> http://www.iplantcollaborative.org/ci/atmosphere

> Upgrade Ubuntu 14.04.02 LTS base VM to Bio-Linux 8
> 
> # start Ubuntu 14.04.2 no GUI base VM and login
> ajtravis at vm64-212:~$ 
> sudo -i
> root at vm64-212:~# 
> 
> wget http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> chmod +x upgrade8.sh
> 
> # capture Bio-Linux 8 upgrade script
> vim upgrade8.sh
> ...
> #cd "`mktemp -d || echo /dev/null`"
> #if [ "$?" != 0 ] ; then
> #  echo "Unable to change to temporary directory; cannot continue."
> #  exit 2
> #fi
> ...
> ./upgrade8.sh |& tee upgrade8.log
> 
> # fix bug when upgrading 'Vanilla' Ubuntu 14.04
> vim upgrade_to_8.sh
> ...
> # If this was run on a Vanilla Ubuntu 14.04 box then Universe/Multiverse sources
> # will not be active.  Tell the user about it.
> if grep -qw universe   /etc/apt/sources.list && \
>    grep -qw multiverse /etc/apt/sources.list ; then
> ...
> 
> # remove conflicting packages
> apt remove gnome-bluetooth
> 
> # upgrade to Bio-Linux 8
> ./upgrade_to_8.sh |& tee upgrade_to_8.log
> ...
> Err http://archive.ubuntu.com/ubuntu/ trusty/universe prank amd64 0.0.140110-1
>   Could not resolve 'archive.ubuntu.com'
> E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/universe/p/prank/prank_0.0.140110-1_amd64.deb  Could not resolve 'archive.ubuntu.com'
> ...
> 
> # restart upgrade
> ./upgrade_to_8.sh
> 
> # ubuntu-desktop installed, but not dependencies
> apt remove ubuntu-desktop
> apt install ubuntu-desktop
> 
> # tidy up /root
> root at vm64-212:~# 
> logout
> ajtravis at vm64-212:~$ 
> sudo rm /root/*
> sudo rm /root/.bash_history
> sudo rm -r /root/.config
> sudo rm /root/.viminfo
> sudo ls -al /root
> total 20
> drwx------  3 root root 4096 Nov 25 08:50 .
> drwxr-xr-x 23 root root 4096 Nov 25 07:36 ..
> drwx------  2 root root 4096 Nov 25 08:26 .aptitude
> -rw-r--r--  1 root root 3106 Feb 19  2014 .bashrc
> -rw-r--r--  1 root root  140 Feb 19  2014 .profile


One way forward is for us to try modifying Tim's Bio-Linux 'upgrade'
script with a view to creating a Debian Bio-Linux meta-package like the
one for "ubuntu-desktop". This will not, of course, provide a new
Bio-Linux 9 'live' DVD, but it would allow us to identify problems and
make remastering an Ubuntu 16.04 LTS .iso image later on much easier.

Bye,

  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 avarus at fastmail.fm  Thu Jan 21 04:38:34 2016
From: avarus at fastmail.fm (Tim Booth)
Date: Thu, 21 Jan 2016 09:38:34 +0000
Subject: [Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?
In-Reply-To: <56A01045.6070203@minke-informatics.co.uk>
References: <1453312880.3248.9.camel@miamioh.edu>
	<56A01045.6070203@minke-informatics.co.uk>
Message-ID: <1453369114.1460607.498361162.60278FAE@webmail.messagingengine.com>

Hi All,

Just to re-iterate what Tony said, I have a new job up in Edinburgh with
a lot to do and a lot to learn.  There is nobody in Wallingford to
inherit the Bio-Linux project so there is no secret master plan for
going forward.

My plan is to concentrate fully on my new job for the next few months,
then think about my next steps for Bio-Linux once I've settled in the
new job.  My senior colleagues here are very supportive when I have
discussed this with them.  In the meantime, I'll be delighted to see any
contributions from the user community or ideas of how people want to
take things forward, and will participate as much as I can.  After all,
I'm still a Bio-Linux user myself!

I've tried upgrading a Bio-Linux 7 machine to the latest Ubuntu and most
things seem to work.  Having said that, most of the important packages
are already in Ubuntu anyway via Debian-Med, so you could just install
vanilla Ubuntu, enable C2D4U to get the R stuff and apt install whatever
bioinformatics packages you need.  Of course, you won't get package
updates either way so you'll be stuck with the current versions of all
the tools.

The discussion seems to have turned to development details so I'll
continue on bio-linux-devel
(http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel).

TIM

On Wed, Jan 20, 2016, at 10:55 PM, Tony Travis wrote:
> On 20/01/16 18:01, Andor J Kiss wrote:
> > Hello,
> > 
> > Does anyone know the future plans for Bio-Linux?  In terms of Bio-Linux
> > 9 & Ubuntu 16.04 LTS?
> 
> Hi, Andor.
> 
> I've already volunteered to help keep the Bio-Linux project rolling, but
> it is unclear what, if any, continuation of EOS/NEBC funding there might
> be to continue supporting Bio-Linux development.
> 
> I think we should let Tim Booth lead the discussion about Bio-Linux 9
> when he has settled into his new job in Edinburgh.
> 
> Meanwhile, we in the Bio-Linux community can continue to provide help
> and support for people who want to use the existing Bio-Linux 8.
> 
> I've had good success using Tim's 'upgrade' script to create physical
> and virtual Bio-Linux instances based on 'standard' Ubuntu 14.04 LTS:
> 
> > http://environmentalomics.org/bio-linux-installation/
> > wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh
> 
> There are some minor problems with the script, but one show-stopper is
> the way Tim's script checks if you have the 'multiverse' repository
> enabled in Ubuntu 14.04 LTS. This is how I did it under OpenStack on
> iPlant Atmosphere recently:
> 
> > http://www.iplantcollaborative.org/ci/atmosphere
> 
> > Upgrade Ubuntu 14.04.02 LTS base VM to Bio-Linux 8
> > 
> > # start Ubuntu 14.04.2 no GUI base VM and login
> > ajtravis at vm64-212:~$ 
> > sudo -i
> > root at vm64-212:~# 
> > 
> > wget http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> > chmod +x upgrade8.sh
> > 
> > # capture Bio-Linux 8 upgrade script
> > vim upgrade8.sh
> > ...
> > #cd "`mktemp -d || echo /dev/null`"
> > #if [ "$?" != 0 ] ; then
> > #  echo "Unable to change to temporary directory; cannot continue."
> > #  exit 2
> > #fi
> > ...
> > ./upgrade8.sh |& tee upgrade8.log
> > 
> > # fix bug when upgrading 'Vanilla' Ubuntu 14.04
> > vim upgrade_to_8.sh
> > ...
> > # If this was run on a Vanilla Ubuntu 14.04 box then Universe/Multiverse sources
> > # will not be active.  Tell the user about it.
> > if grep -qw universe   /etc/apt/sources.list && \
> >    grep -qw multiverse /etc/apt/sources.list ; then
> > ...
> > 
> > # remove conflicting packages
> > apt remove gnome-bluetooth
> > 
> > # upgrade to Bio-Linux 8
> > ./upgrade_to_8.sh |& tee upgrade_to_8.log
> > ...
> > Err http://archive.ubuntu.com/ubuntu/ trusty/universe prank amd64 0.0.140110-1
> >   Could not resolve 'archive.ubuntu.com'
> > E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/universe/p/prank/prank_0.0.140110-1_amd64.deb  Could not resolve 'archive.ubuntu.com'
> > ...
> > 
> > # restart upgrade
> > ./upgrade_to_8.sh
> > 
> > # ubuntu-desktop installed, but not dependencies
> > apt remove ubuntu-desktop
> > apt install ubuntu-desktop
> > 
> > # tidy up /root
> > root at vm64-212:~# 
> > logout
> > ajtravis at vm64-212:~$ 
> > sudo rm /root/*
> > sudo rm /root/.bash_history
> > sudo rm -r /root/.config
> > sudo rm /root/.viminfo
> > sudo ls -al /root
> > total 20
> > drwx------  3 root root 4096 Nov 25 08:50 .
> > drwxr-xr-x 23 root root 4096 Nov 25 07:36 ..
> > drwx------  2 root root 4096 Nov 25 08:26 .aptitude
> > -rw-r--r--  1 root root 3106 Feb 19  2014 .bashrc
> > -rw-r--r--  1 root root  140 Feb 19  2014 .profile
> 
> 
> One way forward is for us to try modifying Tim's Bio-Linux 'upgrade'
> script with a view to creating a Debian Bio-Linux meta-package like the
> one for "ubuntu-desktop". This will not, of course, provide a new
> Bio-Linux 9 'live' DVD, but it would allow us to identify problems and
> make remastering an Ubuntu 16.04 LTS .iso image later on much easier.
> 
> Bye,
> 
>   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/mailman/listinfo/bio-linux-list


-- 
Of course I'm a technophobe; I program computers for a living!