From tony.travis at minke-informatics.co.uk  Tue Aug  8 06:37:48 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 8 Aug 2017 11:37:48 +0100
Subject: [Bio-linux-list] FW: New contact form received
In-Reply-To: <VI1PR0601MB24942CF8C4719393DC515006E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
References: <3b5cbbf1082eaa1ad85e1cd530779e98@environmentalomics.org>
	<VI1PR0601MB24942CF8C4719393DC515006E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
Message-ID: <334f3337-640c-77a4-6a20-a4f23b3da27a@minke-informatics.co.uk>

On 08/08/17 11:03, Timms-Wilson, Tracey wrote:
> [...]
>> You have received a new contact form message.
>> Name : Karla Georges
>> Email : karla.cecile at gmail.com
>> Message : The link to OVA file for use with VirtualBox/VMware , Download
>>from main site is not working

Hi, Karla.

Tracey forwarded your email to me and I've CC'ed it to the Bio-Linux
mailing list in case anyone else has the same problem.

The direct link to the Bio-Linux OVA file is:

> http://nebc.nerc.ac.uk/downloads/bio-linux-8-latest.ova

The current version of the OVA is Bio-Linux-8.0.7:

> http://nebc.nerc.ac.uk/downloads/bio-linux-8.0.7.ova

The same OVA file is mirrored on "ibiblio":

> http://distro.ibiblio.org/bio-linux/iso/bio-linux-8.0.7.ova

It is also available on "Bioinformatics.org":

> https://www.bioinformatics.org/downloads/index.php/bio-linux/bio-linux-8.0.7.ova

And on AWS (Amazon Web Services) S3 (Simple Storage Service):

> https://s3-eu-west-1.amazonaws.com/bio-linux/bio-linux-8.0.7.ova

I've created created a public AMI (Amazon Machine Image) by importing
the Bio-Linux 8.0.7 OVA into EC2 (AWS Elastic Compute Cloud):

   "ami-2dee1954"

We have been working on an 8.0.8 point release of Bio-Linux, which we
are currently testing and will release soon on "Bioinformatics.org":

> https://www.bioinformatics.org/groups/?group_id=341

My student Will McCaffery has been working over the summer to update the
Linux kernel and packages to the current Ubuntu 14.04.05 release, which
has better support for modern hardware - Especially newer WiFi chipsets.

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 tony.travis at minke-informatics.co.uk  Tue Aug  8 07:14:35 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 8 Aug 2017 12:14:35 +0100
Subject: [Bio-linux-list] FW: New contact form received
In-Reply-To: <VI1PR0601MB2494173EBBDDA61F8C2D3CD2E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
References: <6ec3708840a1ba38ead50751b7af8d05@environmentalomics.org>
	<VI1PR0601MB2494173EBBDDA61F8C2D3CD2E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
Message-ID: <4a671e58-a4ea-ca76-d49d-a1e5e404533f@minke-informatics.co.uk>

On 08/08/17 11:57, Timms-Wilson, Tracey wrote:
>> -----Original Message-----
>> From: Steffen Hin [mailto:hinz at biochemie-tud.de]
>> Sent: 24 July 2017 13:57
>> To: Timms-Wilson, Tracey <tmt at ceh.ac.uk>; Timms-Wilson, Tracey
>> <tmt at ceh.ac.uk>
>> Subject: New contact form received
>>
>>
>> You have received a new contact form message.
>> Name : Steffen Hinz
>> Email : hinz at biochemie-tud.de
>> Message : Hi,
>> I just want to know if it is planned to release BioLinux on a newer Ubuntu
>> version (for example 16.04) in the near future.

Hi, Steffen.

Tracey forwarded your email to me and I've CC'ed it to the Bio-Linux
mailing list in case anyone else has the same question.

I've already upgraded several Bio-Linux 8.0.7 machines to Ubuntu 16.04
LTS, but broken packages dependencies mean that a lot of work will be
needed to get everything working. At present, we are seeking funding to
do the necessary work.

The Bio-Linux 8.0.8 point-release that my student Will McCaffery has
been working on will address the main problem with the 'old' Linux
kernel in the current Bio-Linux 8.0.7. However, this will make no
difference to a Bio-Linux 8.0.7 instance installed to disk if you keep
Bio-Linux up-to-date (i.e. not running it from a USB-stick) because it
will then have the same kernel and updated packages as the new 8.0.8:

  # login to an installed Bio-Linux instance and open a terminal
  sudo -i
  apt update
  apt full-upgrade
  apt-get autoremove

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 tony.travis at minke-informatics.co.uk  Tue Aug  8 11:27:21 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 8 Aug 2017 16:27:21 +0100
Subject: [Bio-linux-list] QIIME2 under Bio-Linux 8
In-Reply-To: <1501843715.3627.185.camel@ed.ac.uk>
References: <1501688238.3627.143.camel@ed.ac.uk>
	<7EBCBCD7-FC7A-47FB-AB84-6ACDA066B57E@bangor.ac.uk>
	<1501843715.3627.185.camel@ed.ac.uk>
Message-ID: <4b2eb00c-3d63-e4c0-b2f8-b43a8494e80b@minke-informatics.co.uk>

On 04/08/17 11:48, Tim Booth wrote:
> [...]
> On Thu, 2017-08-03 at 20:49 +0000, Simon Creer wrote:
>> [...]
>> Before I start trying to reinstall QIIME2 on my existing BioLinux
>> sticks I wanted to touch base with you first, to explore whether or
>> not you thought there were better options available? Either because
>> you are already updating BioLinux with Q2 and could let me have some
>> new sticks, or because you may have a more streamlined solution into
>> getting Q2 onto my existing ones?
>> Hoping that you get this mail and if you could get back to me at your
>> earliest convenience, I would be really grateful, many thanks!

Hi, Simon.

Tim forwarded your email to me and I've CC'ed it to the Bio-Linux list
in case anyone else is struggling with QIIME under Bio-Linux.

I installed QIIME 1.9.1 using "bioconda" under Bio-Linux 8.0.7 a while
ago, when helping a colleague who was having problems with the version
installed by default. This is how to install QIIME using "bioconda":

> # install Miniconda to /usr/local/miniconda2
> wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
> bash Miniconda2-latest-Linux-x86_64.sh
> 
> # configure Miniconda for Python 2.7
> export PATH="/usr/local/miniconda2/bin:$PATH"
> conda config --add channels conda-forge
> conda config --add channels defaults
> conda config --add channels r
> conda config --add channels bioconda
> 
> # install QIIME
> conda install qiime
> print_qiime_config.py -t

I then wrote a "wrapper" to prevent "bioconda" breaking the default
Ubuntu 14.04 Python environmment used by Bio-Linux:

> root at wildcat:~# cat /usr/local/bin/bioconda
> #!/bin/bash
> #@(#)bioconda.sh  2017-08-08  A.J.Travis
> 
> #
> # Wrapper for Bioconda Python environment
> #
> 
> # check if already in Bioconda environment
> export BIOCONDA_HOME=/usr/local/miniconda2
> if [[ "$PATH" != *$BIOCONDA_HOME* ]]; then
> 
> 	# added by Miniconda2 4.3.11 installer
> 	export PATH="$BIOCONDA_HOME/bin:$PATH"
> 	debian_chroot=bioconda exec /bin/bash
> fi

You can then run my "bioconda" wrapper to install and use conda:

> root at wildcat:~# bioconda
> (bioconda)root at wildcat:~# 
> conda list qiime
> # packages in environment at /usr/local/miniconda2:
> #
> qiime                     1.9.1               np112py27_1    bioconda
> qiime-default-reference   0.1.3                    py27_0    bioconda

I've followed the instructions to install QIIME2 in bioconda at:

> https://docs.qiime2.org/2017.7/install/native/

This is how I installed it using my "bioconda" wrapper:

> (bioconda)root at wildcat:~# 
> bioconda
> conda update conda
> conda create -n qiime2-2017.7 --file https://data.qiime2.org/distro/core/qiime2-2017.7-conda-linux-64.txt
> source activate qiime2-2017.7

> (bioconda)root at wildcat:~# source activate qiime2-2017.7
> (qiime2-2017.7) (bioconda)root at wildcat:~# conda list qiime2
> # packages in environment at /usr/local/miniconda2/envs/qiime2-2017.7:
> #
> qiime2                    2017.7.0                 py35_0    qiime2/label/r2017.7

The "qiime command now defaults to QIIME2:

> (qiime2-2017.7) (bioconda)root at wildcat:~# qiime --version
> q2cli version 2017.7.0
> Run `qiime info` for more version details.

We've created a Bio-Linux 8.0.8 point-release and are testing the .iso:
I can supply Bio-Linux 8.0.8 sticks commercially if you are interested?

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 mkmodi at aau.ac.in  Thu Aug 10 05:17:18 2017
From: mkmodi at aau.ac.in (Mahendra Modi)
Date: Thu, 10 Aug 2017 14:47:18 +0530
Subject: [Bio-linux-list] FW: New contact form received
In-Reply-To: <4a671e58-a4ea-ca76-d49d-a1e5e404533f@minke-informatics.co.uk>
References: <6ec3708840a1ba38ead50751b7af8d05@environmentalomics.org>
	<VI1PR0601MB2494173EBBDDA61F8C2D3CD2E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
	<4a671e58-a4ea-ca76-d49d-a1e5e404533f@minke-informatics.co.uk>
Message-ID: <CAPUhUGySqCqQcsUR6pLJGGtDvfStkRxTm_0NfOdUXc=2FX97Cg@mail.gmail.com>

Hi,

I upgraded a new installation of Bio-Linux (my desktop - a Dell ystem with
2x i7 processor) to BioLinux 8.0.8 as per instruction provided. Everything
works well. So, most probably I will upgrade my BioLinux servers as well.
However, while running 'apt-get update' I get the following errors. Can
anyone  explain what is happenning here?



Ign http://dl.google.com stable InRelease
Ign http://dl.google.com stable InRelease
Ign http://extras.ubuntu.com trusty InRelease
Ign http://nebc.nerc.ac.uk unstable InRelease
Ign http://www.stats.bris.ac.uk trusty/ InRelease
Ign http://archive.ubuntu.com trusty InRelease
Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_IN
Ign http://extras.ubuntu.com trusty/main Translation-en_IN
Ign http://dl.google.com stable/main Translation-en_IN
Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en
Ign http://extras.ubuntu.com trusty/main Translation-en
Ign http://dl.google.com stable/main Translation-en
Ign http://www.stats.bris.ac.uk trusty/ Translation-en_IN
Ign http://www.stats.bris.ac.uk trusty/ Translation-en
Ign http://archive.ubuntu.com trusty/main Translation-en_IN
Ign http://archive.ubuntu.com trusty/multiverse Translation-en_IN
Ign http://archive.ubuntu.com trusty/restricted Translation-en_IN
Ign http://archive.ubuntu.com trusty/universe Translation-en_IN
W: Failed to fetch
http://dl.google.com/linux/chrome/deb/dists/stable/Release  Unable to find
expected entry 'main/binary-i386/Packages' in Release file (Wrong
sources.list entry or malformed file)

E: Some index files failed to download. They have been ignored, or old ones
used instead.

However, I am not sure whether this is a new phenomenon that can be linked
with BioLinux 8.0.8 or it existed earlier too.

Mahendra


________________________
*Prof. Mahendra K Modi*
*Head, Agril Biotechnology & Coordinator, DIC*
*Assam Agricultural University*
*Jorhat 785013, India*


On Tue, Aug 8, 2017 at 4:44 PM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 08/08/17 11:57, Timms-Wilson, Tracey wrote:
> >> -----Original Message-----
> >> From: Steffen Hin [mailto:hinz at biochemie-tud.de]
> >> Sent: 24 July 2017 13:57
> >> To: Timms-Wilson, Tracey <tmt at ceh.ac.uk>; Timms-Wilson, Tracey
> >> <tmt at ceh.ac.uk>
> >> Subject: New contact form received
> >>
> >>
> >> You have received a new contact form message.
> >> Name : Steffen Hinz
> >> Email : hinz at biochemie-tud.de
> >> Message : Hi,
> >> I just want to know if it is planned to release BioLinux on a newer
> Ubuntu
> >> version (for example 16.04) in the near future.
>
> Hi, Steffen.
>
> Tracey forwarded your email to me and I've CC'ed it to the Bio-Linux
> mailing list in case anyone else has the same question.
>
> I've already upgraded several Bio-Linux 8.0.7 machines to Ubuntu 16.04
> LTS, but broken packages dependencies mean that a lot of work will be
> needed to get everything working. At present, we are seeking funding to
> do the necessary work.
>
> The Bio-Linux 8.0.8 point-release that my student Will McCaffery has
> been working on will address the main problem with the 'old' Linux
> kernel in the current Bio-Linux 8.0.7. However, this will make no
> difference to a Bio-Linux 8.0.7 instance installed to disk if you keep
> Bio-Linux up-to-date (i.e. not running it from a USB-stick) because it
> will then have the same kernel and updated packages as the new 8.0.8:
>
>   # login to an installed Bio-Linux instance and open a terminal
>   sudo -i
>   apt update
>   apt full-upgrade
>   apt-get autoremove
>
> 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 abdn.ac.uk  Thu Aug 10 08:31:05 2017
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 10 Aug 2017 13:31:05 +0100
Subject: [Bio-linux-list] FW: New contact form received
In-Reply-To: <CAPUhUGySqCqQcsUR6pLJGGtDvfStkRxTm_0NfOdUXc=2FX97Cg@mail.gmail.com>
References: <6ec3708840a1ba38ead50751b7af8d05@environmentalomics.org>
	<VI1PR0601MB2494173EBBDDA61F8C2D3CD2E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
	<4a671e58-a4ea-ca76-d49d-a1e5e404533f@minke-informatics.co.uk>
	<CAPUhUGySqCqQcsUR6pLJGGtDvfStkRxTm_0NfOdUXc=2FX97Cg@mail.gmail.com>
Message-ID: <92163402-9e19-1ac2-6d64-1f9f99c8e82b@abdn.ac.uk>

On 10/08/17 10:17, Mahendra Modi wrote:
> Hi,
>
> I upgraded a new installation of Bio-Linux (my desktop - a Dell ystem
> with 2x i7 processor) to BioLinux 8.0.8 as per instruction provided.
> Everything works well. So, most probably I will upgrade my BioLinux
> servers as well. However, while running 'apt-get update' I get the
> following errors. Can anyone  explain what is happenning here?

Hi, Mahendra.

There is a bug in Bio-Linux 8.0.7 caused by an incorrect APT
sources.list entry for Google Chrome. It should be like this:

> cat /etc/apt/sources.list.d/google-chrome.list
> ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
> # You may comment out this entry, but any other modifications may be lost.
> deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main

You need to edit the file, then run the APT commands again:

  apt update
  apt full-upgrade
  apt-get autoremove

You don't need to do this on "Aryabhatta" because I already did :-)

> ajt at Aryabhatta[ajt] cat /etc/apt/sources.list.d/google-chrome.list                                                        [ 5:55PM]
> ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
> # You may comment out this entry, but any other modifications may be lost.
> deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main

And "Aryabhatta" is already upgrades to Ubuntu 14.04.05 LTS:

> ajt at Aryabhatta[ajt] lsb_release -d                                                                                        [ 5:56PM]
> Description:  Ubuntu 14.04.5 LTS

The purpose of the Bio-Linux 8.0.8 release is to make the USB-stick more
compatible with modern hardware (e.g. WiFi chipsets) and to reduce the
number of updates required to be downloaded after installation. If you
keep a Bio-Linux 8 instance up-to-date you will already be running the
equivalent of Bio-Linux 8.0.8.

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

From mkmodi at aau.ac.in  Thu Aug 10 09:49:16 2017
From: mkmodi at aau.ac.in (Mahendra Modi)
Date: Thu, 10 Aug 2017 19:19:16 +0530
Subject: [Bio-linux-list] FW: New contact form received
In-Reply-To: <92163402-9e19-1ac2-6d64-1f9f99c8e82b@abdn.ac.uk>
References: <6ec3708840a1ba38ead50751b7af8d05@environmentalomics.org>
	<VI1PR0601MB2494173EBBDDA61F8C2D3CD2E58A0@VI1PR0601MB2494.eurprd06.prod.outlook.com>
	<4a671e58-a4ea-ca76-d49d-a1e5e404533f@minke-informatics.co.uk>
	<CAPUhUGySqCqQcsUR6pLJGGtDvfStkRxTm_0NfOdUXc=2FX97Cg@mail.gmail.com>
	<92163402-9e19-1ac2-6d64-1f9f99c8e82b@abdn.ac.uk>
Message-ID: <CAPUhUGxCyW=Gs7OS671H7kNxJ0xncBUijG-vc9Q=YzUOZnkB8A@mail.gmail.com>

Thanks Tony.

Mahendra K Modi

On Aug 10, 2017 18:01, "Tony Travis" <tony.travis at abdn.ac.uk> wrote:

> On 10/08/17 10:17, Mahendra Modi wrote:
> > Hi,
> >
> > I upgraded a new installation of Bio-Linux (my desktop - a Dell ystem
> > with 2x i7 processor) to BioLinux 8.0.8 as per instruction provided.
> > Everything works well. So, most probably I will upgrade my BioLinux
> > servers as well. However, while running 'apt-get update' I get the
> > following errors. Can anyone  explain what is happenning here?
>
> Hi, Mahendra.
>
> There is a bug in Bio-Linux 8.0.7 caused by an incorrect APT
> sources.list entry for Google Chrome. It should be like this:
>
> > cat /etc/apt/sources.list.d/google-chrome.list
> > ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
> > # You may comment out this entry, but any other modifications may be
> lost.
> > deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main
>
> You need to edit the file, then run the APT commands again:
>
>   apt update
>   apt full-upgrade
>   apt-get autoremove
>
> You don't need to do this on "Aryabhatta" because I already did :-)
>
> > ajt at Aryabhatta[ajt] cat /etc/apt/sources.list.d/google-chrome.list
>                                                   [ 5:55PM]
> > ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
> > # You may comment out this entry, but any other modifications may be
> lost.
> > deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main
>
> And "Aryabhatta" is already upgrades to Ubuntu 14.04.05 LTS:
>
> > ajt at Aryabhatta[ajt] lsb_release -d
>                                                   [ 5:56PM]
> > Description:  Ubuntu 14.04.5 LTS
>
> The purpose of the Bio-Linux 8.0.8 release is to make the USB-stick more
> compatible with modern hardware (e.g. WiFi chipsets) and to reduce the
> number of updates required to be downloaded after installation. If you
> keep a Bio-Linux 8 instance up-to-date you will already be running the
> equivalent of Bio-Linux 8.0.8.
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> 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 tauqeer9 at gmail.com  Sat Aug 12 00:03:01 2017
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Fri, 11 Aug 2017 23:03:01 -0500
Subject: [Bio-linux-list] WiFi No additional Driver
Message-ID: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>

Hi All
I am trying to set up WiFi connection on my Biolinux machine, but it is not
working. It is not recognising and WiFi connections and any additional
drivers are not appearing either (Systems Settings > Software & Updates >
Additional Drivers). It says "No additional drivers available". Everything
works fine when Ethernet cable is connected.

Any help will be highly appreciated.

Thanks

Tauqeer
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From amalnath.j at gmail.com  Sat Aug 12 00:07:37 2017
From: amalnath.j at gmail.com (Amalnath John)
Date: Fri, 11 Aug 2017 23:07:37 -0500
Subject: [Bio-linux-list] WiFi No additional Driver
In-Reply-To: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
References: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
Message-ID: <CADcWscXwtK-LrE=fH1fLTTLQp3rH4kiNfLBQ+8JDytUNDRNBEw@mail.gmail.com>

Hi,
Can I know the output of ifconfig command?

Regards,
Amalnath

On 11-Aug-2017 11:03 PM, "Tauqeer Alam" <tauqeer9 at gmail.com> wrote:

> Hi All
> I am trying to set up WiFi connection on my Biolinux machine, but it is
> not working. It is not recognising and WiFi connections and any additional
> drivers are not appearing either (Systems Settings > Software & Updates >
> Additional Drivers). It says "No additional drivers available". Everything
> works fine when Ethernet cable is connected.
>
> Any help will be highly appreciated.
>
> Thanks
>
> Tauqeer
>
> _______________________________________________
> 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  Sat Aug 12 05:49:48 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sat, 12 Aug 2017 10:49:48 +0100
Subject: [Bio-linux-list] WiFi No additional Driver
In-Reply-To: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
References: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
Message-ID: <87b3834f-f9d5-6716-7b9f-046b2f2d3220@minke-informatics.co.uk>

On 12/08/17 05:03, Tauqeer Alam wrote:
> Hi All
> I am trying to set up WiFi connection on my Biolinux machine, but it is
> not working. It is not recognising and WiFi connections and any
> additional drivers are not appearing either (Systems Settings > Software
> & Updates > Additional Drivers). It says "No additional drivers
> available". Everything works fine when Ethernet cable is connected.

Hi, Tauqeer.

Please post details of the hardware by running:

  sudo lshw -short

Please also post the output from:

  lsb_release -d

It should say:

  Description:	Ubuntu 14.04.5 LTS

If you have Bio-Linux 8 installed on hard disk, then make sure you do:

  sudo -i
  apt update
  apt full-upgrade
  apt-get autoremove

*** DON'T do this if you're running Bio-Linux from a USB-stick! ***

If you are using a Bio-Linux 8.0.7 USB-stick, it is using an older Linux
kernel from Ubuntu 14.04.02 and may not support more recent WiFi chips.

A work-around is to use a USB WiFi dongle instead of the built-in WiFi.

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 tauqeer9 at gmail.com  Sat Aug 12 10:41:36 2017
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Sat, 12 Aug 2017 09:41:36 -0500
Subject: [Bio-linux-list] WiFi No additional Driver
In-Reply-To: <87b3834f-f9d5-6716-7b9f-046b2f2d3220@minke-informatics.co.uk>
References: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
	<87b3834f-f9d5-6716-7b9f-046b2f2d3220@minke-informatics.co.uk>
Message-ID: <CAFaE85B3rfHqK117tFezZ9X4WvaL1g3S2cpx0BhBJry0p34DkQ@mail.gmail.com>

Thank you very much. I have Bio-Linux 8 installed on hard disk. Here are
the outputs-

nureen at ayesha:~$ sudo lshw -short

[sudo] password for nureen:
H/W path        Device      Class          Description
======================================================
                            system         All Series (All)
/0                          bus            MAXIMUS VII HERO
/0/0                        memory         64KiB BIOS
/0/42                       memory         32GiB System Memory
/0/42/0                     memory         8GiB DIMM DDR3 Synchronous 1600
MHz (0.6 ns)
/0/42/1                     memory         8GiB DIMM DDR3 Synchronous 1600
MHz (0.6 ns)
/0/42/2                     memory         8GiB DIMM DDR3 Synchronous 1600
MHz (0.6 ns)
/0/42/3                     memory         8GiB DIMM DDR3 Synchronous 1600
MHz (0.6 ns)
/0/51                       processor      Intel(R) Core(TM) i7-4790K CPU @
4.00GHz
/0/51/52                    memory         256KiB L1 cache
/0/51/53                    memory         1MiB L2 cache
/0/51/54                    memory         8MiB L3 cache
/0/100                      bridge         4th Gen Core Processor DRAM
Controller
/0/100/1                    bridge         Xeon E3-1200 v3/4th Gen Core
Processor PCI Express x16 Controller
/0/100/2                    display        Xeon E3-1200 v3/4th Gen Core
Processor Integrated Graphics Controller
/0/100/3                    multimedia     Xeon E3-1200 v3/4th Gen Core
Processor HD Audio Controller
/0/100/14                   bus            9 Series Chipset Family USB xHCI
Controller
/0/100/16                   communication  9 Series Chipset Family ME
Interface #1
/0/100/19       eth0        network        Ethernet Connection (2) I218-V
/0/100/1a                   bus            9 Series Chipset Family USB EHCI
Controller #2
/0/100/1b                   multimedia     9 Series Chipset Family HD Audio
Controller
/0/100/1c                   bridge         9 Series Chipset Family PCI
Express Root Port 1
/0/100/1c.3                 bridge         9 Series Chipset Family PCI
Express Root Port 4
/0/100/1c.3/0               storage        ASM1062 Serial ATA Controller
/0/100/1d                   bus            9 Series Chipset Family USB EHCI
Controller #1
/0/100/1f                   bridge         9 Series Chipset Family Z97 LPC
Controller
/0/100/1f.2                 storage        9 Series Chipset Family SATA
Controller [AHCI Mode]
/0/100/1f.3                 bus            9 Series Chipset Family SMBus
Controller
/0/1            scsi3       storage
/0/1/0.0.0      /dev/sda    disk           2TB WDC WD2002FAEX-0
/0/1/0.0.0/1    /dev/sda1   volume         29GiB Linux swap volume
/0/1/0.0.0/2    /dev/sda2   volume         1833GiB Extended partition
/0/1/0.0.0/2/5  /dev/sda5   volume         1833GiB Linux filesystem
partition
/0/2            scsi4       storage
/0/2/0.0.0      /dev/cdrom  disk           DVDRAM GH24NS95
/0/3            scsi5       storage
/0/3/0.0.0      /dev/sdb    disk           128GB Samsung SSD 840
/0/3/0.0.0/1    /dev/sdb1   volume         954MiB EXT4 volume
/0/3/0.0.0/2    /dev/sdb2   volume         118GiB Linux filesystem partition
/0/4            scsi6       storage
/0/4/0.0.0      /dev/sdc    disk           128GB Samsung SSD 840
/0/4/0.0.0/1    /dev/sdc1   volume         954MiB EXT4 volume
/0/4/0.0.0/2    /dev/sdc2   volume         118GiB Linux filesystem partition
/0/5            scsi7       storage
/0/5/0.0.0      /dev/sdd    disk           2TB WDC WD2002FAEX-0
/0/5/0.0.0/1    /dev/sdd1   volume         1863GiB EXT4 volume
/1                          power          To Be Filled By O.E.M.

nureen at ayesha:~$  lsb_release -d

Description: Ubuntu 14.04.5 LTS

nureen at ayesha:~# ifconfig

eth0      Link encap:Ethernet  HWaddr 54:a0:50:e6:54:53
          inet addr:192.168.0.6  Bcast:192.168.0.255  Mask:255.255.255.0
          inet6 addr: 2601:240:8300:c330:56a0:50ff:fee6:5453/64 Scope:Global
          inet6 addr: fe80::56a0:50ff:fee6:5453/64 Scope:Link
          inet6 addr: 2601:240:8300:c330:31fa:ae36:a71c:7125/64 Scope:Global
          inet6 addr: 2601:240:8300:c330::5/128 Scope:Global
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:68468 errors:0 dropped:0 overruns:0 frame:0
          TX packets:32944 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:98005737 (98.0 MB)  TX bytes:3112093 (3.1 MB)
          Interrupt:20 Memory:f7d00000-f7d20000

lo        Link encap:Local Loopback
          inet addr:127.0.0.1  Mask:255.0.0.0
          inet6 addr: ::1/128 Scope:Host
          UP LOOPBACK RUNNING  MTU:65536  Metric:1
          RX packets:619 errors:0 dropped:0 overruns:0 frame:0
          TX packets:619 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1
          RX bytes:53093 (53.0 KB)  TX bytes:53093 (53.0 KB)

*I also ran following commands-*
  sudo -i
  apt update
  apt full-upgrade
  apt-get autoremove

Thanks

Tauqeer



On Sat, Aug 12, 2017 at 4:49 AM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 12/08/17 05:03, Tauqeer Alam wrote:
> > Hi All
> > I am trying to set up WiFi connection on my Biolinux machine, but it is
> > not working. It is not recognising and WiFi connections and any
> > additional drivers are not appearing either (Systems Settings > Software
> > & Updates > Additional Drivers). It says "No additional drivers
> > available". Everything works fine when Ethernet cable is connected.
>
> Hi, Tauqeer.
>
> Please post details of the hardware by running:
>
>   sudo lshw -short
>
> Please also post the output from:
>
>   lsb_release -d
>
> It should say:
>
>   Description:  Ubuntu 14.04.5 LTS
>
> If you have Bio-Linux 8 installed on hard disk, then make sure you do:
>
>   sudo -i
>   apt update
>   apt full-upgrade
>   apt-get autoremove
>
> *** DON'T do this if you're running Bio-Linux from a USB-stick! ***
>
> If you are using a Bio-Linux 8.0.7 USB-stick, it is using an older Linux
> kernel from Ubuntu 14.04.02 and may not support more recent WiFi chips.
>
> A work-around is to use a USB WiFi dongle instead of the built-in WiFi.
>
> 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  Sat Aug 12 11:18:08 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sat, 12 Aug 2017 16:18:08 +0100
Subject: [Bio-linux-list] WiFi No additional Driver
In-Reply-To: <CAFaE85B3rfHqK117tFezZ9X4WvaL1g3S2cpx0BhBJry0p34DkQ@mail.gmail.com>
References: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
	<87b3834f-f9d5-6716-7b9f-046b2f2d3220@minke-informatics.co.uk>
	<CAFaE85B3rfHqK117tFezZ9X4WvaL1g3S2cpx0BhBJry0p34DkQ@mail.gmail.com>
Message-ID: <89873996-045c-b962-f224-c77c2d1b0e32@minke-informatics.co.uk>

On 12/08/17 15:41, Tauqeer Alam wrote:
> Thank you very much. I have Bio-Linux 8 installed on hard disk. Here are
> the outputs-
> 
> nureen at ayesha:~$ sudo lshw -short
> 
> [sudo] password for nureen: 
> H/W path        Device      Class          Description
> ======================================================
>                             system         All Series (All)
> /0                          bus            MAXIMUS VII HERO
> [...]

Hi, Tauqeer.

I've looked at the manual for you motherboard and it doesn't appear to
have built-in WiFI, unless you're using a different model, which might
explain why it doesn't work:

> http://dlcdnet.asus.com/pub/ASUS/mb/LGA1150/MAXIMUS-VII-HERO/E9799_MAXIMUS_VII_HERO_V2_WEB.pdf

Let me know if this is the correct motherboard model and, if you've
fitted a WiFi card or dongle let me know what type. This is not a
Bio-Linux issue, it's an Ubuntu issue because Bio-Linux is based on
Ubuntu. It might be worth having a look for bug-reports about this.

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 tauqeer9 at gmail.com  Sat Aug 12 13:23:29 2017
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Sat, 12 Aug 2017 12:23:29 -0500
Subject: [Bio-linux-list] WiFi No additional Driver
In-Reply-To: <89873996-045c-b962-f224-c77c2d1b0e32@minke-informatics.co.uk>
References: <CAFaE85CwydSSVA83XD5vD57u4KgorTsXPz1sip1sZmj_B3HocQ@mail.gmail.com>
	<87b3834f-f9d5-6716-7b9f-046b2f2d3220@minke-informatics.co.uk>
	<CAFaE85B3rfHqK117tFezZ9X4WvaL1g3S2cpx0BhBJry0p34DkQ@mail.gmail.com>
	<89873996-045c-b962-f224-c77c2d1b0e32@minke-informatics.co.uk>
Message-ID: <CAFaE85CGi2bOT6a9MzTqd-+xPqNm8h9UVJVYBZuxQt1geick7g@mail.gmail.com>

Hi Tony
Yes, the mother does not have a built-in Wi-Fi adaptor. I have always been
using Ethernet cable so I never knew that it does not exist. Thanks for
pointing this out. I really appreciate your help.

Best wishes

Tauqeer

On Sat, Aug 12, 2017 at 10:18 AM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 12/08/17 15:41, Tauqeer Alam wrote:
> > Thank you very much. I have Bio-Linux 8 installed on hard disk. Here are
> > the outputs-
> >
> > nureen at ayesha:~$ sudo lshw -short
> >
> > [sudo] password for nureen:
> > H/W path        Device      Class          Description
> > ======================================================
> >                             system         All Series (All)
> > /0                          bus            MAXIMUS VII HERO
> > [...]
>
> Hi, Tauqeer.
>
> I've looked at the manual for you motherboard and it doesn't appear to
> have built-in WiFI, unless you're using a different model, which might
> explain why it doesn't work:
>
> > http://dlcdnet.asus.com/pub/ASUS/mb/LGA1150/MAXIMUS-VII-
> HERO/E9799_MAXIMUS_VII_HERO_V2_WEB.pdf
>
> Let me know if this is the correct motherboard model and, if you've
> fitted a WiFi card or dongle let me know what type. This is not a
> Bio-Linux issue, it's an Ubuntu issue because Bio-Linux is based on
> Ubuntu. It might be worth having a look for bug-reports about this.
>
> 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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