From anton.gossner at roslin.ed.ac.uk  Mon Dec  3 04:27:11 2012
From: anton.gossner at roslin.ed.ac.uk (GOSSNER Anton)
Date: Mon, 3 Dec 2012 09:27:11 +0000
Subject: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
In-Reply-To: <1354295581.7749.45.camel@balisaur>
References: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk>,
	<1354295581.7749.45.camel@balisaur>
Message-ID: <4B2DE8422AF25D40820C088EF2AE5D27216883C45B@EXSEEDMD.is.ed.ac.uk>

Hi Tim,

gossnera at gossnera-desktop[gossnera] dpkg -s python-biopython          [ 9:25AM]
Package: python-biopython
Status: install ok installed
Priority: optional
Section: python
Installed-Size: 5835
Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
Architecture: amd64
Version: 1.58-1
Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
Provides: python2.7-biopython
Depends: python (<< 2.8), python (>= 2.7), python-support (>= 0.90.0), libc6 (>= 2.4), python-numpy, python-reportlab
Recommends: python-biopython-doc (= 1.58-1)
Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2
Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
Description: Python library for bioinformatics
 The Biopython Project is an international association
 of developers of freely available Python tools for
 computational molecular biology.
 .
 It is a distributed collaborative effort to develop Python
 libraries and applications which address the needs of
 current and future work in bioinformatics. The source code
 is made available under the Biopython License, which is
 extremely liberal and compatible with almost every license
 in the world. We work along with the Open Bioinformatics
 Foundation, who generously provide web and CVS space for
 the project.
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Homepage: http://biopython.org
Python-Version: 2.7
gossnera at gossnera-desktop[gossnera]                                                                                     [ 9:25AM]

















________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth [tbooth at ceh.ac.uk]
Sent: 30 November 2012 17:13
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Upgrading to Bio-Linux 7 from 6

Hi Anton,

This is more likely a problem with my script than with your system, or
rather there is some minor issue and my script is making a meal of it.

What do you get when you ask dpkg specifically about biopython? - ie:

dpkg -s python-biopython

Also the thing with removing and reinstalling t-coffee is expected -
it's a crude workaround to a problem someone spotted during beta
testing.

Cheers,

TIM

On Fri, 2012-11-30 at 10:40 +0000, GOSSNER Anton wrote:
> Hi,
>
> Just wondered if anybody is having the same problem and has solved it or if need to do a full install.
>
> Following Tims instructions for upgrading, all gone well with initial upgrade of Ubuntu and start of Bio-Linux packages but always stops and exits with;
>
> Verifying that everything installed...
> python-biopython  failed to install
> python-biopython-doc  failed to install
> Not all packages installed properly - exiting.
>
> despite the fact python is installed;
>
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> python-software-properties is already the newest version.
>
>
> Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling  python but to no avail also run "apt-get autoremove"
>
> No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script.
>
> Anton

--
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://nebc.nerc.ac.uk
+44 1491 69 2705
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



From tbooth at ceh.ac.uk  Mon Dec  3 06:58:27 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 3 Dec 2012 11:58:27 +0000
Subject: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
In-Reply-To: <4B2DE8422AF25D40820C088EF2AE5D27216883C45B@EXSEEDMD.is.ed.ac.uk>
References: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk>
	, <1354295581.7749.45.camel@balisaur>
	<4B2DE8422AF25D40820C088EF2AE5D27216883C45B@EXSEEDMD.is.ed.ac.uk>
Message-ID: <1354535907.7749.64.camel@balisaur>

Hi Anton,

I had a good look at the script and realised a couple of rogue spaces
had crept in at the end of two of the lines, which effectively made the
script buggy and caused these errors.  I'm surprised nobody else is
complaining, but in any case I've now fixed that problem.  How's it
looking at your end?

Cheers,

TIM


On Mon, 2012-12-03 at 09:27 +0000, GOSSNER Anton wrote:
> Hi Tim,
> 
> gossnera at gossnera-desktop[gossnera] dpkg -s python-biopython          [ 9:25AM]
> Package: python-biopython
> Status: install ok installed
> Priority: optional
> Section: python
> Installed-Size: 5835
> Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
> Architecture: amd64
> Version: 1.58-1
> Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
> Provides: python2.7-biopython
> Depends: python (<< 2.8), python (>= 2.7), python-support (>= 0.90.0), libc6 (>= 2.4), python-numpy, python-reportlab
> Recommends: python-biopython-doc (= 1.58-1)
> Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2
> Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
> Description: Python library for bioinformatics
>  The Biopython Project is an international association
>  of developers of freely available Python tools for
>  computational molecular biology.
>  .
>  It is a distributed collaborative effort to develop Python
>  libraries and applications which address the needs of
>  current and future work in bioinformatics. The source code
>  is made available under the Biopython License, which is
>  extremely liberal and compatible with almost every license
>  in the world. We work along with the Open Bioinformatics
>  Foundation, who generously provide web and CVS space for
>  the project.
> Original-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
> Homepage: http://biopython.org
> Python-Version: 2.7
> gossnera at gossnera-desktop[gossnera]                                                                                     [ 9:25AM]
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ________________________________________
> From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth [tbooth at ceh.ac.uk]
> Sent: 30 November 2012 17:13
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
> 
> Hi Anton,
> 
> This is more likely a problem with my script than with your system, or
> rather there is some minor issue and my script is making a meal of it.
> 
> What do you get when you ask dpkg specifically about biopython? - ie:
> 
> dpkg -s python-biopython
> 
> Also the thing with removing and reinstalling t-coffee is expected -
> it's a crude workaround to a problem someone spotted during beta
> testing.
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2012-11-30 at 10:40 +0000, GOSSNER Anton wrote:
> > Hi,
> >
> > Just wondered if anybody is having the same problem and has solved it or if need to do a full install.
> >
> > Following Tims instructions for upgrading, all gone well with initial upgrade of Ubuntu and start of Bio-Linux packages but always stops and exits with;
> >
> > Verifying that everything installed...
> > python-biopython  failed to install
> > python-biopython-doc  failed to install
> > Not all packages installed properly - exiting.
> >
> > despite the fact python is installed;
> >
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > python-software-properties is already the newest version.
> >
> >
> > Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling  python but to no avail also run "apt-get autoremove"
> >
> > No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script.
> >
> > Anton
> 
> --
> 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://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From anton.gossner at roslin.ed.ac.uk  Mon Dec  3 08:43:05 2012
From: anton.gossner at roslin.ed.ac.uk (GOSSNER Anton)
Date: Mon, 3 Dec 2012 13:43:05 +0000
Subject: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
In-Reply-To: <1354535907.7749.64.camel@balisaur>
References: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk>	,
	<1354295581.7749.45.camel@balisaur>
	<4B2DE8422AF25D40820C088EF2AE5D27216883C45B@EXSEEDMD.is.ed.ac.uk>
	<1354535907.7749.64.camel@balisaur>
Message-ID: <4B2DE8422AF25D40820C088EF2AE5D27216883D452@EXSEEDMD.is.ed.ac.uk>

Hi Tim,

Completed fine now thanks. Working fine so far. The start up splash screen is still the Bio-Linux 6 logo, doesn't bother me but just checking if that's correct or is my install missing something?

Anton


A Gossner PhD 

The Roslin Institute & R(D)SVS
University of Edinburgh 
Easter Bush 
Midlothian 
EH25 9RG 

A.Gossner at ed.ac.uk 
Tel. No. 0131 6519238 or 6519382


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: 03 December 2012 11:58
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Upgrading to Bio-Linux 7 from 6

Hi Anton,

I had a good look at the script and realised a couple of rogue spaces had crept in at the end of two of the lines, which effectively made the script buggy and caused these errors.  I'm surprised nobody else is complaining, but in any case I've now fixed that problem.  How's it looking at your end?

Cheers,

TIM


On Mon, 2012-12-03 at 09:27 +0000, GOSSNER Anton wrote:
> Hi Tim,
> 
> gossnera at gossnera-desktop[gossnera] dpkg -s python-biopython          [ 9:25AM]
> Package: python-biopython
> Status: install ok installed
> Priority: optional
> Section: python
> Installed-Size: 5835
> Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
> Architecture: amd64
> Version: 1.58-1
> Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 
> 1.42-1)
> Provides: python2.7-biopython
> Depends: python (<< 2.8), python (>= 2.7), python-support (>= 0.90.0), 
> libc6 (>= 2.4), python-numpy, python-reportlab
> Recommends: python-biopython-doc (= 1.58-1)
> Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2
> Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 
> 1.42-1)
> Description: Python library for bioinformatics  The Biopython Project 
> is an international association  of developers of freely available 
> Python tools for  computational molecular biology.
>  .
>  It is a distributed collaborative effort to develop Python  libraries 
> and applications which address the needs of  current and future work 
> in bioinformatics. The source code  is made available under the 
> Biopython License, which is  extremely liberal and compatible with 
> almost every license  in the world. We work along with the Open 
> Bioinformatics  Foundation, who generously provide web and CVS space 
> for  the project.
> Original-Maintainer: Debian Med Packaging Team 
> <debian-med-packaging at lists.alioth.debian.org>
> Homepage: http://biopython.org
> Python-Version: 2.7
> gossnera at gossnera-desktop[gossnera]                                                                                     [ 9:25AM]
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ________________________________________
> From: bio-linux-bounces at nebclists.nerc.ac.uk 
> [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth 
> [tbooth at ceh.ac.uk]
> Sent: 30 November 2012 17:13
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
> 
> Hi Anton,
> 
> This is more likely a problem with my script than with your system, or 
> rather there is some minor issue and my script is making a meal of it.
> 
> What do you get when you ask dpkg specifically about biopython? - ie:
> 
> dpkg -s python-biopython
> 
> Also the thing with removing and reinstalling t-coffee is expected - 
> it's a crude workaround to a problem someone spotted during beta 
> testing.
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2012-11-30 at 10:40 +0000, GOSSNER Anton wrote:
> > Hi,
> >
> > Just wondered if anybody is having the same problem and has solved it or if need to do a full install.
> >
> > Following Tims instructions for upgrading, all gone well with 
> > initial upgrade of Ubuntu and start of Bio-Linux packages but always 
> > stops and exits with;
> >
> > Verifying that everything installed...
> > python-biopython  failed to install
> > python-biopython-doc  failed to install Not all packages installed 
> > properly - exiting.
> >
> > despite the fact python is installed;
> >
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > python-software-properties is already the newest version.
> >
> >
> > Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling  python but to no avail also run "apt-get autoremove"
> >
> > No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script.
> >
> > Anton
> 
> --
> 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://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 

--
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://nebc.nerc.ac.uk
+44 1491 69 2705
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


From tbooth at ceh.ac.uk  Mon Dec  3 08:56:37 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 3 Dec 2012 13:56:37 +0000
Subject: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
In-Reply-To: <4B2DE8422AF25D40820C088EF2AE5D27216883D452@EXSEEDMD.is.ed.ac.uk>
References: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk>
	, <1354295581.7749.45.camel@balisaur>
	<4B2DE8422AF25D40820C088EF2AE5D27216883C45B@EXSEEDMD.is.ed.ac.uk>
	<1354535907.7749.64.camel@balisaur>
	<4B2DE8422AF25D40820C088EF2AE5D27216883D452@EXSEEDMD.is.ed.ac.uk>
Message-ID: <1354542997.7749.72.camel@balisaur>

Hi Anton,

Ah, good point.  I did make the new theme but forgot to link it to the
new themes package.  I've done it now so you should see the new logo
installing when you next update.

Cheers,

TIM

On Mon, 2012-12-03 at 13:43 +0000, GOSSNER Anton wrote:
> Hi Tim,
> 
> Completed fine now thanks. Working fine so far. The start up splash
> screen is still the Bio-Linux 6 logo, doesn't bother me but just
> checking if that's correct or is my install missing something?
> 
> Anton
> 
> 
> A Gossner PhD 
> 
> The Roslin Institute & R(D)SVS
> University of Edinburgh 
> Easter Bush 
> Midlothian 
> EH25 9RG 
> 
> A.Gossner at ed.ac.uk 
> Tel. No. 0131 6519238 or 6519382
> 
> 

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From Jonathan.Davoren at bodetech.com  Wed Dec  5 11:54:32 2012
From: Jonathan.Davoren at bodetech.com (Davoren, Jonathan)
Date: Wed, 5 Dec 2012 16:54:32 +0000
Subject: [Bio-Linux] RDP to biolinux
Message-ID: <A573710B7763194B8A68742156B7723210155E17@BODEVM-EX01.corp.solutionpoint-intl.com>

I have biolinux 7 installed in a Virtual Machine - Windows Server 2003 with Vsphere.  Within Vsphere biolinux works great.

Trying to connect via RDP from windows 7 64 bit remote desktop connection but the RDP continuously says failed to connect.

The exact same setup for the Ubuntu 64 bit 12.04 is working fine.

Installing the NX application on biolinux and the Windows computer allows authentication and starts downloading the connection information and then shows connection error.

Is there some extra security in Biolinux?  Or some configuration that we need to change to be able to get remote access?


Thank you
Jon


Jonathan Davoren
Director, Applied Research & Core Facility
The Bode Technology Group
[cid:bodelogo]
10430 Furnace Rd., Suite 107
Lorton, Virginia 22079 USA
Telephone: +1 703-646-9774
Fax: +1 703-646-9741
Mobile: +1 (571) 246-7175

Jonathan.Davoren at bodetech.com<mailto:Jonathan.Davoren at bodetech.com>

www.bodetech.com<http://www.bodetech.com> | Sign up for the Bode e-Newsletter<http://visitor.r20.constantcontact.com/manage/optin/ea?v=001sG2XUya07KrTvvTvv_I8DQ%3D%3D>



A SolutionPoint International, Inc. Company

www.solutionpoint-intl.com<http://www.solutionpoint-intl.com/>


This message may contain confidential information that may also be defined as U.S. Government export controlled technical data and is intended only for the individual or entity named. It may also be attorney client privileged or otherwise protected as attorney work product. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message. No employee or agent is authorized to conclude any binding agreement on behalf of SolutionPoint International, Inc. or any of its subsidiaries solely via the contents of an email message. If verification is required please request a hard-copy version or contract attachment. IRS Circular 230 Notice: IRS Circular 230 requires that we advise you that any U.S. Federal Tax advice contained in the communication or in any attachment hereto is not intended or written to be used, and cannot be used, for purpose of (I) avoiding penalties under the internal revenue code or (II) promoting, marketing or recommending to another party any transaction or matter addressed herein.

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From tbooth at ceh.ac.uk  Wed Dec  5 13:41:00 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 5 Dec 2012 18:41:00 +0000
Subject: [Bio-Linux] RDP to biolinux
In-Reply-To: <A573710B7763194B8A68742156B7723210155E17@BODEVM-EX01.corp.solutionpoint-intl.com>
References: <A573710B7763194B8A68742156B7723210155E17@BODEVM-EX01.corp.solutionpoint-intl.com>
Message-ID: <1354732860.3061.40.camel@balisaur>

Hi Jonathan,

Bio-Linux comes with a firewall enabled, controlled by the standard ufw
system.  You can configure it by using ufw on the command line or the
graphical gufw application, but on a VM you probably just want to
apt-get uninstall ufw completely and then check that all firewall rules
are gone using 'sudo iptables -L'.

NX is supposed to work out-of-the-box and only needs port 22, same as
SSH.  Do you get any other hints as to why NX fails?  Eg. anything
in /var/log/auth.log on the VM?

Cheers,

TIM

On Wed, 2012-12-05 at 16:54 +0000, Davoren, Jonathan wrote:
> I have biolinux 7 installed in a Virtual Machine - Windows Server 2003
> with Vsphere.  Within Vsphere biolinux works great.
> 
>  
> 
> Trying to connect via RDP from windows 7 64 bit remote desktop
> connection but the RDP continuously says failed to connect.
> 
>  
> 
> The exact same setup for the Ubuntu 64 bit 12.04 is working fine.
> 
>  
> 
> Installing the NX application on biolinux and the Windows computer
> allows authentication and starts downloading the connection
> information and then shows connection error.
> 
>  
> 
> Is there some extra security in Biolinux?  Or some configuration that
> we need to change to be able to get remote access?
> 
>  
> 
>  
> 
> Thank you
> 
> Jon
> 
> 
> 
>  
> 
> Jonathan Davoren
> 
> Director, Applied Research & Core Facility
> 
> The Bode Technology Group
> 
> 
> 
> 10430 Furnace Rd., Suite 107
> 
> Lorton, Virginia 22079 USA
> 
> Telephone: +1 703-646-9774
> 
> Fax: +1 703-646-9741
> 
> Mobile: +1 (571) 246-7175
> 
> Jonathan.Davoren at bodetech.com
> 
> www.bodetech.com | Sign up for the Bode e-Newsletter
> 
>  
> 
> A SolutionPoint International, Inc. Company
> 
> www.solutionpoint-intl.com
> 
>  
> 
> This message may contain confidential information that may also be
> defined as U.S. Government export controlled technical data and is
> intended only for the individual or entity named. It may also be
> attorney client privileged or otherwise protected as attorney work
> product. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail by mistake and
> delete this e-mail from your system. E-mail transmission cannot be
> guaranteed to be secure or error-free as information could be
> intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
> contain viruses. The sender therefore does not accept liability for
> any errors or omissions in the contents of this message. No employee
> or agent is authorized to conclude any binding agreement on behalf of
> SolutionPoint International, Inc. or any of its subsidiaries solely
> via the contents of an email message. If verification is required
> please request a hard-copy version or contract attachment. IRS
> Circular 230 Notice: IRS Circular 230 requires that we advise you that
> any U.S. Federal Tax advice contained in the communication or in any
> attachment hereto is not intended or written to be used, and cannot be
> used, for purpose of (I) avoiding penalties under the internal revenue
> code or (II) promoting, marketing or recommending to another party any
> transaction or matter addressed herein.
> 
> 

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From Matt.Belcher at bodetech.com  Wed Dec  5 13:41:59 2012
From: Matt.Belcher at bodetech.com (Belcher, Matt)
Date: Wed, 5 Dec 2012 18:41:59 +0000
Subject: [Bio-Linux] RDP to biolinux
In-Reply-To: <1354732860.3061.40.camel@balisaur>
References: <A573710B7763194B8A68742156B7723210155E17@BODEVM-EX01.corp.solutionpoint-intl.com>
	<1354732860.3061.40.camel@balisaur>
Message-ID: <1F30D0889D12834DA41BA05DE7C71726E17557@BODEVM-EX01.corp.solutionpoint-intl.com>

Ahh I see, Thanks Tim that?s good to know. 

-----Original Message-----
From: Tim Booth [mailto:tbooth at ceh.ac.uk] 
Sent: Wednesday, December 05, 2012 1:41 PM
To: Bio-Linux help and discussion
Cc: Belcher, Matt; Davoren, Jonathan
Subject: Re: [Bio-Linux] RDP to biolinux

Hi Jonathan,

Bio-Linux comes with a firewall enabled, controlled by the standard ufw system.  You can configure it by using ufw on the command line or the graphical gufw application, but on a VM you probably just want to apt-get uninstall ufw completely and then check that all firewall rules are gone using 'sudo iptables -L'.

NX is supposed to work out-of-the-box and only needs port 22, same as SSH.  Do you get any other hints as to why NX fails?  Eg. anything in /var/log/auth.log on the VM?

Cheers,

TIM

On Wed, 2012-12-05 at 16:54 +0000, Davoren, Jonathan wrote:
> I have biolinux 7 installed in a Virtual Machine - Windows Server 2003 
> with Vsphere.  Within Vsphere biolinux works great.
> 
>  
> 
> Trying to connect via RDP from windows 7 64 bit remote desktop 
> connection but the RDP continuously says failed to connect.
> 
>  
> 
> The exact same setup for the Ubuntu 64 bit 12.04 is working fine.
> 
>  
> 
> Installing the NX application on biolinux and the Windows computer 
> allows authentication and starts downloading the connection 
> information and then shows connection error.
> 
>  
> 
> Is there some extra security in Biolinux?  Or some configuration that 
> we need to change to be able to get remote access?
> 
>  
> 
>  
> 
> Thank you
> 
> Jon
> 
> 
> 
>  
> 
> Jonathan Davoren
> 
> Director, Applied Research & Core Facility
> 
> The Bode Technology Group
> 
> 
> 
> 10430 Furnace Rd., Suite 107
> 
> Lorton, Virginia 22079 USA
> 
> Telephone: +1 703-646-9774
> 
> Fax: +1 703-646-9741
> 
> Mobile: +1 (571) 246-7175
> 
> Jonathan.Davoren at bodetech.com
> 
> www.bodetech.com | Sign up for the Bode e-Newsletter
> 
>  
> 
> A SolutionPoint International, Inc. Company
> 
> www.solutionpoint-intl.com
> 
>  
> 
> This message may contain confidential information that may also be 
> defined as U.S. Government export controlled technical data and is 
> intended only for the individual or entity named. It may also be 
> attorney client privileged or otherwise protected as attorney work 
> product. If you are not the named addressee you should not 
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> transaction or matter addressed herein.
> 
> 

--
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://nebc.nerc.ac.uk
+44 1491 69 2705

From stephane at abgenomica.com  Thu Dec  6 09:43:43 2012
From: stephane at abgenomica.com (Stephane Bortzmeyer)
Date: Thu, 6 Dec 2012 15:43:43 +0100
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
Message-ID: <20121206144343.GA2380@laperouse.bortzmeyer.org>

I try to install biolinux on an existing Ubuntu 12.04. For several
packages, I get:

# apt-get install bio-linux-ape
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 bio-linux-ape:i386 : Depends: bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable
E: Unable to correct problems, you have held broken packages.


But I have bio-linux-base-directories, and at a more recent version:

# apt-cache show bio-linux-base-directories
Package: bio-linux-base-directories
Priority: optional
Section: science
Installed-Size: 3488
Maintainer: Bela Tiwari <helpdesk at envgen.nox.ac.uk>
Architecture: all
Version: 1.0-37

I even checked the version numbers:

# if dpkg --compare-versions 1.0-37 '>=' 1.0-1; then echo OK; fi
OK

I am now completely lost. What is apt-get expecting?


From tbooth at ceh.ac.uk  Thu Dec  6 10:56:53 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 6 Dec 2012 15:56:53 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <20121206144343.GA2380@laperouse.bortzmeyer.org>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
Message-ID: <1354809413.3061.111.camel@balisaur>

Hi Stephane,

Thanks for trying Bio-Linux.  The explanation for this problem is that
there are old packages on the server that no longer work but I've
neglected to clean them out as they were wanted by some users of older
systems.  Ape is one such package.  Ubuntu 10.04 wouldn't see this
package at all as it is i386/32-bit but 12.04 tries to install it anyway
and then it wants an i386 compatibility library that doesn't exist.

If you have Ubuntu 12.04, you should install the package
bio-linux-shared, which will force you to remove
bio-linux-base-directories.  Anything which insists on putting
bio-linux-base-directories back is a legacy package and either
superseded or no longer supported.  I'm going to try and sort these
things out and clear out the junk now that the initial BL7 release is
out of the way.

If you just want to run ape, we're no longer specifically supporting
that package but installing is very easy.  Just start R on the command
line and type:

install.packages('ape')

In general, I'm only putting R packages on our server now if a non-R
package depends on them or if they are particularly tricky to set up.

Cheers,

TIM

On Thu, 2012-12-06 at 14:43 +0000, Stephane Bortzmeyer wrote:
> I try to install biolinux on an existing Ubuntu 12.04. For several
> packages, I get:
> 
> # apt-get install bio-linux-ape
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
> 
> The following packages have unmet dependencies:
>  bio-linux-ape:i386 : Depends: bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable
> E: Unable to correct problems, you have held broken packages.
> 
> 
> But I have bio-linux-base-directories, and at a more recent version:
> 
> # apt-cache show bio-linux-base-directories
> Package: bio-linux-base-directories
> Priority: optional
> Section: science
> Installed-Size: 3488
> Maintainer: Bela Tiwari <helpdesk at envgen.nox.ac.uk>
> Architecture: all
> Version: 1.0-37
> 
> I even checked the version numbers:
> 
> # if dpkg --compare-versions 1.0-37 '>=' 1.0-1; then echo OK; fi
> OK
> 
> I am now completely lost. What is apt-get expecting?
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From stephane at abgenomica.com  Thu Dec  6 14:43:06 2012
From: stephane at abgenomica.com (Stephane Bortzmeyer)
Date: Thu, 6 Dec 2012 20:43:06 +0100
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <1354809413.3061.111.camel@balisaur>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>
Message-ID: <20121206194306.GA25825@sources.org>

On Thu, Dec 06, 2012 at 03:56:53PM +0000,
 Tim Booth <tbooth at ceh.ac.uk> wrote 
 a message of 84 lines which said:

> Ape is one such package.  Ubuntu 10.04 wouldn't see this package at
> all as it is i386/32-bit but 12.04 tries to install it anyway and
> then it wants an i386 compatibility library that doesn't exist.

OK, I understand, thanks for the explanations (I just used the script
from
<https://github.com/mchelen/bio-linux-tools/blob/master/bio-linux-install.sh>,
which includes many of these obsolete packages.)

> If you have Ubuntu 12.04, you should install the package
> bio-linux-shared, which will force you to remove
> bio-linux-base-directories.

Done.

> Anything which insists on putting bio-linux-base-directories back is
> a legacy package and either superseded or no longer supported.

bio-linux-emboss for instance :-(



From tony.travis at ed.ac.uk  Thu Dec  6 15:16:35 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 06 Dec 2012 20:16:35 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <20121206194306.GA25825@sources.org>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>
	<20121206194306.GA25825@sources.org>
Message-ID: <50C0FD23.6080206@ed.ac.uk>

On 06/12/12 19:43, Stephane Bortzmeyer wrote:
> On Thu, Dec 06, 2012 at 03:56:53PM +0000,
>   Tim Booth <tbooth at ceh.ac.uk> wrote
>   a message of 84 lines which said:
>
>> Ape is one such package.  Ubuntu 10.04 wouldn't see this package at
>> all as it is i386/32-bit but 12.04 tries to install it anyway and
>> then it wants an i386 compatibility library that doesn't exist.
>
> OK, I understand, thanks for the explanations (I just used the script
> from
> <https://github.com/mchelen/bio-linux-tools/blob/master/bio-linux-install.sh>,
> which includes many of these obsolete packages.)
>
>> If you have Ubuntu 12.04, you should install the package
>> bio-linux-shared, which will force you to remove
>> bio-linux-base-directories.
>
> Done.
>
>> Anything which insists on putting bio-linux-base-directories back is
>> a legacy package and either superseded or no longer supported.
>
> bio-linux-emboss for instance :-(

Hi, Stephane and Tim.

It's not just "bio-linux-emboss", these packages all depend on 
"bio-linux-base-directories:

bio-linux-emboss
bio-linux-estscan
bio-linux-prank
bio-linux-qiime
bio-linux-rdp-classifier
bio-linux-seaview
bio-linux-transterm-hp
bio-linux-trnascan
bio-linux-wise2

I'm struggling to get my Bio-Linux 7 system "aptitude -f install" clean, 
but can't install these packages from the NEBC repository. The previous 
versions installed were flagged as "local or obsolete" in Synaptic, so I 
forced the version (before Tim's earlier post to the list). I'm 
comparing the package lists on my system with the casper manifest of 
Bio-Linux 7.0.2.

Bye,

   Tony.




From tony.travis at ed.ac.uk  Thu Dec  6 19:59:16 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Fri, 07 Dec 2012 00:59:16 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <50C0FD23.6080206@ed.ac.uk>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>
	<20121206194306.GA25825@sources.org> <50C0FD23.6080206@ed.ac.uk>
Message-ID: <50C13F64.10205@ed.ac.uk>

On 06/12/12 20:16, Tony Travis wrote:
> [...] I'm
> comparing the package lists on my system with the casper manifest of
> Bio-Linux 7.0.2.

Hi, Tim.

There are duplicate entries in the casper filesystem manifests:

> sort bio-linux-7.0.2-filesystem.manifest | uniq -d | wc -l
> 211
> sort bio-linux-7.0.2-filesystem.manifest-desktop | uniq -d | wc -l
> 211

Is this a mistake?

It hinders my checks, so I've corrected the filesystem manifests:

> mv -i bio-linux-7.0.2-filesystem.manifest bio-linux-7.0.2-filesystem.manifest.orig
> sort bio-linux-7.0.2-filesystem.manifest.orig | uniq >bio-linux-7.0.2-filesystem.manifest
> mv -i bio-linux-7.0.2-filesystem.manifest-desktop.new bio-linux-7.0.2-filesystem.manifest-desktop.orig
> sort bio-linux-7.0.2-filesystem.manifest-desktop.orig | uniq >bio-linux-7.0.2-filesystem.manifest

I'm using "manifest-desktop" to verify that Bio-Linux installations done 
using your "bio-linux-install.sh" upgrade script are equivalent to 
installations done directly from the .iso release. I'm only checking the 
package names, not their versions, using the "dpkg-dsel" script that I 
wrote to validate Bio-Linux 6 installations the same way.

Bye,

   Tony.


From tbooth at ceh.ac.uk  Fri Dec  7 04:37:29 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 7 Dec 2012 09:37:29 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <50C0FD23.6080206@ed.ac.uk>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>	<20121206194306.GA25825@sources.org>
	<50C0FD23.6080206@ed.ac.uk>
Message-ID: <1354873049.3061.133.camel@balisaur>

Hi Tony,


> I'm struggling to get my Bio-Linux 7 system "aptitude -f install" clean, 
> but can't install these packages from the NEBC repository. The previous 
> versions installed were flagged as "local or obsolete" in Synaptic, so I 
> forced the version (before Tim's earlier post to the list). I'm 
> comparing the package lists on my system with the casper manifest of 
> Bio-Linux 7.0.2.

I can go and push all the new packages to the server today, which will
save you from having to see a warning that packages might be "local",
but I warn you - all your NBX users on 10.04 are going to get a whole
lot of nasty warnings appearing.  Is that OK?

Otherwise my suggestion would be to re-run my installer script and let
it clean things up for you:
http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh


Cheers,

TIM

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From A.J.Pemberton at bham.ac.uk  Fri Dec  7 04:43:49 2012
From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton)
Date: Fri, 7 Dec 2012 09:43:49 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <1354873049.3061.133.camel@balisaur>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>	<20121206194306.GA25825@sources.org>
	<50C0FD23.6080206@ed.ac.uk> <1354873049.3061.133.camel@balisaur>
Message-ID: <5FAE4EF51F20774D9C21A133494A3FE02330A49571@LESMBX1.adf.bham.ac.uk>

Tim,

Does this mean that bio-linux 6 users should eliminate the nebc repo in their sources.list?

Regards,

Tony Pemberton


-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: 07 December 2012 09:37
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Cannot install on Ubuntu "Depends: bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"

Hi Tony,


> I'm struggling to get my Bio-Linux 7 system "aptitude -f install" 
> clean, but can't install these packages from the NEBC repository. The 
> previous versions installed were flagged as "local or obsolete" in 
> Synaptic, so I forced the version (before Tim's earlier post to the 
> list). I'm comparing the package lists on my system with the casper 
> manifest of Bio-Linux 7.0.2.

I can go and push all the new packages to the server today, which will save you from having to see a warning that packages might be "local", but I warn you - all your NBX users on 10.04 are going to get a whole lot of nasty warnings appearing.  Is that OK?

Otherwise my suggestion would be to re-run my installer script and let it clean things up for you:
http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh


Cheers,

TIM

--
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://nebc.nerc.ac.uk
+44 1491 69 2705
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


From tbooth at ceh.ac.uk  Fri Dec  7 04:52:03 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 7 Dec 2012 09:52:03 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE02330A49571@LESMBX1.adf.bham.ac.uk>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>	<20121206194306.GA25825@sources.org>
	<50C0FD23.6080206@ed.ac.uk> <1354873049.3061.133.camel@balisaur>
	<5FAE4EF51F20774D9C21A133494A3FE02330A49571@LESMBX1.adf.bham.ac.uk>
Message-ID: <1354873923.3061.139.camel@balisaur>

Hi Tony P,

Possibly.  I can reassure you that nothing is going to break, and system
security updates from Ubuntu will continue to install, but you will get
warnings because APT will see new packages it thinks it should install
but can't satisfy the dependencies.  Since I'm not planning on adding
any new software to BL6 from now on, you may as well turn off the repo
to hide the warnings.

Cheers,

TIM

On Fri, 2012-12-07 at 09:43 +0000, Anthony Pemberton wrote:
> Tim,
> 
> Does this mean that bio-linux 6 users should eliminate the nebc repo
> in their sources.list?
> 
> Regards,
> 
> Tony Pemberton



From tony.travis at ed.ac.uk  Fri Dec  7 17:47:19 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Fri, 07 Dec 2012 22:47:19 +0000
Subject: [Bio-Linux] Cannot install on Ubuntu "Depends:
 bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"
In-Reply-To: <1354873049.3061.133.camel@balisaur>
References: <20121206144343.GA2380@laperouse.bortzmeyer.org>
	<1354809413.3061.111.camel@balisaur>	<20121206194306.GA25825@sources.org>
	<50C0FD23.6080206@ed.ac.uk> <1354873049.3061.133.camel@balisaur>
Message-ID: <50C271F7.7030503@ed.ac.uk>

On 07/12/12 09:37, Tim Booth wrote:
> Hi Tony,
>
>
>> I'm struggling to get my Bio-Linux 7 system "aptitude -f install" clean,
>> but can't install these packages from the NEBC repository. The previous
>> versions installed were flagged as "local or obsolete" in Synaptic, so I
>> forced the version (before Tim's earlier post to the list). I'm
>> comparing the package lists on my system with the casper manifest of
>> Bio-Linux 7.0.2.
>
> I can go and push all the new packages to the server today, which will
> save you from having to see a warning that packages might be "local",
> but I warn you - all your NBX users on 10.04 are going to get a whole
> lot of nasty warnings appearing.  Is that OK?

Hi, Tim.

I downloaded your debs from:

   http://nebc.nerc.ac.uk/downloads/bl7_only

And re-installed them on my laptop manually using "gdebi"

I think it's time to upgrade the NBX's - We are planning to move them 
all to Milan soon anyway, and build an OpenStack cloud to run virtual 
NBX's instead. For now, I'll leave them running Bio-Linux 6.

Bye,

   Tony.


From stephane at abgenomica.com  Wed Dec 19 05:17:22 2012
From: stephane at abgenomica.com (Stephane Bortzmeyer)
Date: Wed, 19 Dec 2012 11:17:22 +0100
Subject: [Bio-Linux] Galaxy in the apt repository???
Message-ID: <20121219101722.GA10826@laperouse.bortzmeyer.org>

I've noticed that Bio-Linux 7 includes Galaxy but I cannot find it in
the NEBC apt repository.

I have this sources.list:

% cat /etc/apt/sources.list.d/nebc.nox.ac.uk.bio-linux.sources.list 
deb http://nebc.nox.ac.uk/bio-linux/ unstable bio-linux

And yet, no Galaxy available:

% apt-cache search galaxy
uqm - The Ur-Quan Masters - An inter-galatic adventure game
[And only other irrelevant stuff]


From tbooth at ceh.ac.uk  Wed Dec 19 06:52:53 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 19 Dec 2012 11:52:53 +0000
Subject: [Bio-Linux] Galaxy in the apt repository???
In-Reply-To: <20121219101722.GA10826@laperouse.bortzmeyer.org>
References: <20121219101722.GA10826@laperouse.bortzmeyer.org>
Message-ID: <1355917973.10304.186.camel@balisaur>

Hi Stephane,

The Bio-Linux packages now straddle two repositories, with the newer
stuff on Launchpad.net.  You need to add both sources.  Please see this
page:

http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository

Also, any references to "nebc.nox.ac.uk" need to be changed to
"nebc.nerc.ac.uk" as the old DNS entries will be removed in the near
future.

Be aware that the Galaxy package is a work in progress.  It does mostly
work OK but the tool-shed feature is not happy due to permissions issues
and setting up the database and administrator account is not as simple
as we would like it to be.  We also need to write more documentation.

Cheers,

TIM

On Wed, 2012-12-19 at 10:17 +0000, Stephane Bortzmeyer wrote:
> I've noticed that Bio-Linux 7 includes Galaxy but I cannot find it in
> the NEBC apt repository.
> 
> I have this sources.list:
> 
> % cat /etc/apt/sources.list.d/nebc.nox.ac.uk.bio-linux.sources.list 
> deb http://nebc.nox.ac.uk/bio-linux/ unstable bio-linux
> 
> And yet, no Galaxy available:
> 
> % apt-cache search galaxy
> uqm - The Ur-Quan Masters - An inter-galatic adventure game
> [And only other irrelevant stuff]
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From tbooth at ceh.ac.uk  Fri Dec 21 12:32:46 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 21 Dec 2012 17:32:46 +0000
Subject: [Bio-Linux] A Unity Lens (ie. a better applications menu) for
	Bio-Linux
Message-ID: <1356111166.7339.14.camel@balisaur>

Dear All,

How are Bio-Linux 7 users getting on with the new Unity desktop
interface?  After using it for several months now I've got quite used to
it, especially after learning a few keyboard shortcuts.  The most
essential is Ctrl+Alt+<Arrow key> to switch between the virtual
desktops, as using the switcher icon is a pain.  I also like the
enhanced Alt+Tab functionality.

Once of the shortcomings of the current Bio-Linux 7 desktop is that,
since the old heirarchical applications menu is not shown in Unity,
there is no good way to see a list of bioinformatics applications.  I
put a folder of applications on the desktop but this is only good for a
stop-gap measure and only works for new user accounts.  I've therefore
taken a few days while things are quiet before Christmas and I've made a
package that adds a bioinformatics section (or a lens, as they are
called) into the main menu panel.  It looks like this:

http://nebc.nerc.ac.uk/downloads/bl7_only/newlens.jpg

To install it, apt-get install bio-linux-unity-lens, then log out and
back in again.  Of course, this is only going to work if you use Unity,
so users of NX need not apply.  I hope this is useful.  Any comments?

Cheers,

TIM

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From stephane at abgenomica.com  Fri Dec 21 17:04:43 2012
From: stephane at abgenomica.com (Stephane Bortzmeyer)
Date: Fri, 21 Dec 2012 23:04:43 +0100
Subject: [Bio-Linux] Galaxy in the apt repository???
In-Reply-To: <1355917973.10304.186.camel@balisaur>
References: <20121219101722.GA10826@laperouse.bortzmeyer.org>
	<1355917973.10304.186.camel@balisaur>
Message-ID: <20121221220443.GA25574@sources.org>

On Wed, Dec 19, 2012 at 11:52:53AM +0000,
 Tim Booth <tbooth at ceh.ac.uk> wrote 
 a message of 56 lines which said:

> The Bio-Linux packages now straddle two repositories, with the newer
> stuff on Launchpad.net.  You need to add both sources.  Please see this
> page:
> 
> http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository

Thanks, it works and the documentation is clear.


From damien.zammit at gmail.com  Wed Dec 26 03:11:58 2012
From: damien.zammit at gmail.com (Damien Zammit)
Date: Wed, 26 Dec 2012 19:11:58 +1100
Subject: [Bio-Linux] A Unity Lens (ie. a better applications menu) for
	Bio-Linux
In-Reply-To: <1356111166.7339.14.camel@balisaur>
References: <1356111166.7339.14.camel@balisaur>
Message-ID: <CABXa2sEGD_Zr8_erLsJs=8NKZvajpqyEPYtEUHme79PsgSUh5g@mail.gmail.com>

On 22 December 2012 04:32, Tim Booth <tbooth at ceh.ac.uk> wrote:
> taken a few days while things are quiet before Christmas and I've made a
> package that adds a bioinformatics section (or a lens, as they are
> called) into the main menu panel.  It looks like this:

Hi there,
I realise I am just a single user and my opinion doesn't count for
much in terms of a survey of user opinions.  However, for what it's
worth, it has come to my attention that Canonical have been collecting
information about what people search for in the Unity search bar and
your Ubuntu computer sends this information to Amazon for marketing
purposes automatically.
I'm so disappointed by this feature that I made the switch to Debian,
since the presence of this feature circumvents the freedom of a user
to their privacy.

Regards,
Damien


From sasa.paporovic at fh-bielefeld.de  Wed Dec 26 09:25:01 2012
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Wed, 26 Dec 2012 15:25:01 +0100
Subject: [Bio-Linux] A Unity Lens (ie. a better applications menu) for
 Bio-Linux
In-Reply-To: <CABXa2sEGD_Zr8_erLsJs=8NKZvajpqyEPYtEUHme79PsgSUh5g@mail.gmail.com>
References: <1356111166.7339.14.camel@balisaur>
	<CABXa2sEGD_Zr8_erLsJs=8NKZvajpqyEPYtEUHme79PsgSUh5g@mail.gmail.com>
Message-ID: <27940_1356531901_ZZi0b7Gm8gJMH.00_fbfdd46e6222.50db16cd@fh-bielefeld.de>

The switch to Debian is one possibility, but you can also do on a terminal

sudo apt-get remove unity-lens-shopping

This deletes the component(unity shopping lens) of the unity desktop that causes the information traffic to amazon and canonical.

BTW: AFAIK Biolinux 7 is based on Ubuntu12.04(Precise). In this version is no unity shopping lens. It was first introduced at the end of the development phase of Ubuntu12.10(Quantal). With this it has never reached Biolinux.

----- Original Message -----
From: Damien Zammit <damien.zammit at gmail.com>
Date: Wednesday, December 26, 2012 9:12
Subject: Re: [Bio-Linux] A Unity Lens (ie. a better applications menu) for Bio-Linux
To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>

> On 22 December 2012 04:32, Tim Booth <tbooth at ceh.ac.uk> wrote:
> > taken a few days while things are quiet before Christmas and 
> I've made a
> > package that adds a bioinformatics section (or a lens, as they are
> > called) into the main menu panel.  It looks like this:
> 
> Hi there,
> I realise I am just a single user and my opinion doesn't count for
> much in terms of a survey of user opinions.  However, for 
> what it's
> worth, it has come to my attention that Canonical have been collecting
> information about what people search for in the Unity search bar and
> your Ubuntu computer sends this information to Amazon for marketing
> purposes automatically.
> I'm so disappointed by this feature that I made the switch to Debian,
> since the presence of this feature circumvents the freedom of a user
> to their privacy.
> 
> Regards,
> Damien
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
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