From tbooth at ceh.ac.uk  Fri May  3 05:11:49 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 3 May 2013 10:11:49 +0100
Subject: [Bio-Linux] [Fwd: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu]
In-Reply-To: <1364463746.3208.538.camel@balisaur>
References: <1364463746.3208.538.camel@balisaur>
Message-ID: <1367572309.20970.658.camel@balisaur>

Dear R users,

Further to my last message, Michael Rutter is now in the process of
upgrading the R packages to 3.0.0.  As far as I can tell, the upgrade
will be fairly smooth with the following important caveats:

1) All locally installed modules will need to be refreshed and rebuilt
by the system administrator (or the user if installed in the home dir).
Users of Bioconductor in particular will need to do this.  See the notes
here:

http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor#rpack

2) I have prepared updated DEB packages for all the R libraries that
install this way, but there may be a day or two when these are out of
sync with the core R packages.  You will then see warnings from the
update manager that updates cannot be applied.  Give it a couple of days
and this should all be straightened out.

If you are not sure if this applies to you then there's no need to be
paranoid.  R will complain loudly and clearly if you try to load an
incompatible module, and you will be in no doubt that you need to update
it.

Cheers,

TIM

On Thu, 2013-03-28 at 09:42 +0000, Tim Booth wrote:
> Dear Bio-Linux Users,
> 
> The message below is relevant to anyone who uses R.  The basic gist is
> that you have until 1st May to decide if you want to upgrade to the
> latest R 3.0.0 or stay with R 2.15 on your system for now.  You will
> have to take some action either way.  I'll prepare some specific
> instructions for Bio-Linux users when Michael releases more info but you
> should start to think about this now.
> 
> This page lists the changes in version 3.0.0:
> http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html
> 
> If you do not use R, or if you only use R as part of a larger package
> like Galaxy, this change will hopefully not trouble you.  I will do some
> testing here to ensure there are no unexpected knock-on effects from the
> upgrade for non R users.
> 
> Cheers,
> 
> TIM
> 
> 
> -------- Forwarded Message --------
> From: Michael Rutter <mar36 at psu.edu>
> Reply-to: "mar36 at psu.edu" <mar36 at psu.edu>
> To: r-sig-debian at r-project.org <r-sig-debian at r-project.org>
> Subject: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu
> Date: Wed, 27 Mar 2013 20:08:16 +0000
> 
> This is a post I just added to my Ubuntu R Blog 
> (http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/2013/03/moving-to-r-300-on-ubuntu.html).
> 
> As you may (or may not) be aware of, R 3.0.0 is [scheduled to be 
> released](http://www.r-project.org/) on April 3rd.  Since this is a 
> major release and there may be some growing pains (but I hope not) in 
> the move 3.0.0, here is some information about how I will handle R 3.0.0 
> on CRAN and my PPAs for Ubuntu.
> 
> **All packages must be rebuilt for R 3.0.0**
> 
> Any installed packages you are currently using will have to be rebuilt 
> using R 3.0.0.  This could lead to some issues, especially is you are 
> using the Ubuntu binaries on CRAN or my PPA.  I will try to minimize 
> these issues.
> 
> **CRAN and RRutter PPA are now frozen to R 2.15.3 (with one exception)**
> 
> Since many users would probably be alarmed to have production machines 
> upgrade to R 3.0.0 without testing to see if any thing breaks, the 
> packages on [CRAN](http://cran.us.r-project.org/bin/linux/ubuntu/) and 
> the [RRutter PPA](https://launchpad.net/~marutter/+archive/rrutter) will 
> not be updated anymore.  This means R is frozen with version 2.15.3 and 
> the packages available will not be updated on CRAN or the RRutter PPA 
> for now.
> 
> At some point, likely around May 1st, I will move CRAN and the RRutter 
> PPA to version 3.0.0.  This should give users plenty of time to remove 
> those repositories from apt so the upgrades do not occur.  I will warn 
> everyone when I am about to do this.
> 
> The one exception to this rule will be the forth coming Ubuntu 13.04 
> (Raring Ringtail).  When I add this release to CRAN and the PPA, I will 
> be using R 3.0.0 and packages built against 3.0.0.
> 
> **R 3.0.0 and recommended packages will be available on RDev PPA**
> 
> If you do want to upgrade R to 3.0.0, you can use my [RDdev 
> PPA](https://launchpad.net/~marutter/+archive/rdev).  This will have the 
> latest version of R and the recommended packages built against it. 
> Instructions on how to install the PPA are available at the  [RDdev 
> PPA](https://launchpad.net/~marutter/+archive/rdev) webpage.  As of 
> right now, only 12.10 (quantal) builds are available, but others will be 
> added when bugs are worked out.  Please, do not have the RDev PPA and 
> (CRAN or RRutter PPA) enabled at the same time, as that could cause issues.
> 
> **What about c2d4u?**
> 
> Excellent question.
> 
> **Stopping support for Hardy and Oneiric**
> 
> Both Hardy (8.04) and Oneiric (11.10) are ending support in April 2013. 
>   Therefore, I will not be updating any version of R for these releases. 
>   I, for one, am happy to finally be able to rid myself of the albatross 
> (or should I say heron) that is Hardy.  I will not delete these files 
> for a while, but there will be no further updates.  Support for Lucid 
> (10.04) will continue until April 2015 or until something becomes very 
> broken.
> 
> **Are you sure you don't have anything to say about c2d4u?**
> 
> [c2d4u](https://launchpad.net/~marutter/+archive/c2d4u) is an ambitious 
> project that houses over 1000 packages for R as Ubuntu binaries that can 
> be installed via apt or synaptic.  You should really check it out. It 
> has great packages like RCpp and ggplot2, among others.
> 
> My first priority will be is to build all the packages for Ubuntu 13.04 
> (Raring Ringtail) using R 3.0.0.  After that is complete, I will start 
> rebuilding the packages for 12.04 (Precise), the latest LTS, against 
> 3.0.0.  If I still have any patience left, I will convert the 12.10 
> (Quantal) packages over.
> 
> If you have any questions, please email me.
> 
> Michael
> -- 
> Dr. Michael A. Rutter
> School of Science
> Penn State Erie, The Behrend College
> Station Road
> Erie, PA 16563
> http://math.bd.psu.edu/faculty/rutter
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> 

-- 
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 sasa.paporovic at fh-bielefeld.de  Sat May  4 13:24:28 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Sat, 04 May 2013 19:24:28 +0200
Subject: [Bio-Linux] Announcing the Backport of Concavity from Ubuntu 13.04
	to Biolinux 7
Message-ID: <29675_1367688268_ZZi0m2jp4QhmX.00_fc32e3e61468.5185606c@fh-bielefeld.de>

Announcing the Backport of Concavity from Ubuntu 13.04 to Biolinux 7

To summarize the content, here is a short list what will be to read here:

1. What is concavity?

2. What is the genealogy between Ubuntu 13.04 and Biolinux 7
(Could be skipped for fully informed people)?

3. What is a backport?

4. How to get it now?!

5.Can we get more backports for the newest software in bioinformatics?


If you are only interested in to get it working, this mail and mail 4 is important to you and the rest must not be read.

If you are interested in read about the future in Mail 5 it is better to read Mail 2 and Mail 3 first, before you start with Mail 5. 

For short:

Concavity is a slim command line program for predicting ligand binding sites of proteins.

What is that good for:

One of the major issues for drug development in any way is to have a clue what kind of substances could bound to a protein.

For in silico prediction on this(e.g with AutoDock4 or its successor autodock-vina) it is helpful to reduce the protein surface to just that parts where an interaction is possible at all. This are the ligand binding sites of a protein.

There are sevaral algorithms available for this. E.g. Ligsite, Surfnet or Pocket finder. or...
Also webservices are there, which can do the job:
LigsiteCS, QsiteFinder, CASTp,... other.

Concavity arises arround 2009(yes, we are a little bit slow) with a new algorithmic approach as can be seen in:

?Predicting Protein Ligand Binding Sites by Combining Evolutionary  Sequence Conservation and 3D Structure? by John A. Capra et al. , PLOS, 2009 

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000585

PDF available in open Access(right site download button).

!Concavity reaches up to 80% prediction success!

, which is remarkable more than the webservices like CASTp, QsiteFinder and Ligsite, as can be seen in Fig.4 on page 7 in the paper of Capra, cited above.

The best webserver prediction was up to 60%(precision).

Conclusion:

80% precision with concavity v.s. 60% precision with established methods.

=>That should be brought to the heart of the bioinformatics community.

I have felt free to do do that via backporting.

The concavity package is already available via software-center in Biolinux 7. 

!Important!

!The additional package conservation-code is available too. It do the precalculations that are needed for concavity to reach the 80% precision! 


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From sasa.paporovic at fh-bielefeld.de  Sat May  4 13:36:21 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Sat, 04 May 2013 19:36:21 +0200
Subject: [Bio-Linux] Mail2:The question arises from where comes the software
 and how comes it to Biolinux 7
Message-ID: <15496_1367688982_ZZi0m1jI745dd.00_fc4cf1022220.51856335@fh-bielefeld.de>

To2: The question arises from where comes the software and how comes it to Biolinux 7 ?

For this let us see where the source is.

Mostly it begins on Debian Linux. There is a team that call itself Debian-Med:

http://wiki.debian.org/DebianMed

Andreas Tille is one of the most active members.
They decide in the best of there knowledge what bioinformatic software is good for Debian and, properly more remarkable, they do the packaging and system integration job.

S. M?ller, H. N. Krabbenh?ft, A. Tille, D. Paleino, A. Williams, K. Wolstencroft, C. Goble, R. Holland, D. Belhachemi, C. Plessy (2010) "Community-driven computational biology with Debian Linux" BMC Bioinformatics, 11(Suppl 12):S5 

A. Tille, S. M?ller, M. Hanke, Y. Halchenko (2011) "Debian Med - Integrated software environment for all medical purposes based on Debian GNU/Linux", Med at Tel 2011

[Please cite them also if you use the bio-software on Ubuntu]


?And how comes Ubuntu in the game??

Ubuntu is a bit parasitic to Debian. Oh, let me correct that. It is a symbiont.
They derive the Software for the actual development branch of Ubuntu(just finished Ubuntu13.04 development) from the actual testing branch of Debian(it was from Debian 7 testing).

The other way around Ubuntu provide problem information and bugfixes for the Debian project. Additional many Ubuntu developers are also Debian developers(or the other way around).

To user terms of genealogy:

Debian is the mother and Ubuntu the daughter.

?And what is the relation to Biolinux??

Tim Boot(grandmaster level) and team(grandmaster level) do the same as the Ubuntu people with Debian. They derive, but not from Debian direct. Instead they derive from Ubuntu long term supported Versions - > Ubuntu LTS(10.04 for Biolinux 6; 12.04 for Biolinux 7) 

With this Debian ist the grandmother, Ubuntu the mother and Biolinux the douther.

Field, D., Tiwari, B., Booth, T., Houten, S., Swan, D., Bertrand, N. and Thurston, M. 2006. Open Software for biologists: from famine to feast. Nature Biotechnology 24, 801 - 803. 

So, to summaries the game:

Sourcecode(bio) --Andreas Tille et al.-->Debian(sooner or later in testing)

--Ubuntu developers--> Ubuntu LTS(all even years;the .04 version)

--Tim Booth et al.-->Biolinux

The reader with attention have recognized that there are only every two(even) years are Ubuntu LTS-Versions(6.06 in 2006, 8.04 in April,10.04 in April 2010, 12.04 in April 2012 and the next will be 14.04 in year 2014 ? you see xx.04 means April as release date for final).

That is not good to get only every two years fresh scientific sofware/software versions, which is the consequence of the fact that Biolinux is derived only on the LTS versions and their 2 year release cycle.

Keep cool you will be helped!

Tim(and grandmaster-team) are incorporating additional software in Biolinux and bring new software version on over there own repository:

http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux

, which is enabled by default in Biolinux.

They give also back to Ubuntu and Debian and prepare with this also the next versions).

Wow, what a job!

Is this now all?

No, there is still a other bridge on which new software could migrate into Biolinux.

Let us have a look.

? Mail3: What is a backport?



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From sasa.paporovic at fh-bielefeld.de  Sat May  4 14:08:09 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Sat, 04 May 2013 20:08:09 +0200
Subject: [Bio-Linux] Mail3:What is a backport?
Message-ID: <15494_1367690890_ZZi0m1jLc4wdK.00_fc609c561b1c.51856aa9@fh-bielefeld.de>

To3: What is a backport?

Your Biolinux7-System gather its software from different servers/sources, called repositories.

Some of them are the original repositories for Ubuntu12.04, from which Biolinux is derived.


BTW:

If you want to have a direct look on which repositories are enabled on your system, you find the configuration file in:

/etc/apt/

it is called 

sources.list

,but beware, do not change it manually, I have seen this in Ubuntu answer section

https://answers.launchpad.net/ubuntu

and Ubuntu bugtracker

https://bugs.launchpad.net/ubuntu

to often failing.

One other repository is direct from the Biolinux team and provide the software that makes Biolinux to Biolinux.

The last is:

http://nebc.nerc.ac.uk/bio-linux/

More comfortable you can get a html view of the available software here:

http://nebc.nerc.ac.uk/tools/bio-linux/package-list

Now let us have a look at the original Ubuntu12.04 repositories.

By default following repositories are enabled for Ubuntu 12.04(it is called ?Precise pangolin?; Mark Shuttleworth has the tendence to give animal names..., well, no further comment):

deb http://de.archive.ubuntu.com/ubuntu/ precise

[Do not try this in your webbrowser, that will fail. What you see here is apt format]

followed by a space and(not complete list)

main
universe
multiverse
security
backports

Aha, there we have: backports

Let us have a short look at the others:

main:
provide the core of the Ubuntu12.04/Biolinux, like the kernel(linux3.2.x), the unity desktop, LibreOffice,...,
well all what a standard system needs and the Ubuntu Core developers put their hands on.

Universe:
Yes, this is the stuff for us. The brave, the geeks, the... scientists.
Most of the scientific software we use reside in universe.
The packages from the Debian-Med project(you remember:...Tille), for example.

Unfortunately the Ubuntu Core developers do not put hands on this(in general).
The cause is that there is more software out there than developers, so they focus on the main repository to provide a maintained core system.

A other BTW:

If you decide to work on this packages for the benefit of all of us, you can find a software QA page created by the Debian-Med team, that point also to the bugs in Ubuntu bugtracker:

http://qa.debian.org/developer.php?login=debian-med-packaging at lists.alioth.debian.org&ordering=3

and here is a good developer guide to get started:

https://wiki.ubuntu.com/UbuntuDevelopment

[I know Ubuntu best; this is the cause for links to that project. Debian has also good material to get started: have a google]

, but beware. This is the deep look with the long journey. Nothing for a weekend, nothing for short term enthusiasm. You count here in month.
Multiverse:
Here reside the software, where is doubt if it is really free software.
Sometimes it is clear that the Software is non-free. Sometimes the software only depends on non-free components.

Security:
Also Linux is attacable,like through an old browser version. For this and to bypass the common introducing procedure of fixes, which needs a little bit longer, the security repository was introduced.
A small team of the Ubuntu developers are allowed to work direct on this.
For you it is at most relevant for e.g firefox, thunderbird and so on.
Every new version of this by nature security exposed software comes through the security repository.


Uff, finaly we are there. The backports repository.

Backports:
For short: It brings newest software to you. 
Ubuntu(the mother of Biolinux) is at most strictly oriented forward. So, the big bunch of worktime of the Ubuntu Core developers are going into the actual development branch(just finished Ubuntu13.04 raring).
What you get in the older (final) releases, those which are still supported, is what is falling from the desk.
If a fix in the actual development fits also for a problem in one of the previous final releases the patch will also brought there.
The rest of the system of final releases will be kept untouched. There is no special further development on.
On LTS versions, like Ubuntu 12.04(you know it: It is the basis for Biolinux7)the support period is 5 years, in the style described above.

!No newer software will be get into Biolinux in this style!

For getting arround this the backport repository was introduced.

You know, the development of Ubuntu-Linux is more a evolutionary one. There are mostly no hard breaks. You have the opportunity to upgrade from one Ubuntu release version to another. You see this more directly on the distribution upgrade capability from Biolinux6 to Biolinux 7 (based on the upgrade capabilities between Ubuntu 10.04 LTS and Ubuntu12.04 LTS).

And there fits backporting.

Even when you use(and you really should - more stability, better scientific validity through fixes of not obvious calculation/results errors in scientific software) the distribution upgrade, there is a period of waiting around 2 years until you can do that(until the new LTS is final).

For bridging over this gap, we have the backporting repository.

The process of backporting is driven by the community people like you and me and start with looking what is there at software for the latest development branch of Ubuntu(just finished raring, just started saucy).

It follows manually downloading the Package and setting up some  virtualmachines for testing if the package for Raring is also working on older Releases of Ubuntu.

There is a online dokumentation to the backporting process:

https://wiki.ubuntu.com/UbuntuBackports


Ubuntu13.04(just finished development version Raring) ? using ubuntu-dev-tools for build for Quantal(Ubuntu12.10) and Precise(Ubuntu12.04) ? manually install the result packages in a virtualMachine of Ubuntu12.10 Quantal ? manually install the resulting packages in a VirtualMachine of Ubuntu12.04 Precise ? use ubuntu-dev-tools to request a backport ? prepare the ticket that targets on this on launchpad ? if accepted for Ubuntu12.10 Quantal and Ubuntu12.04 Precise ? Hits Bilinux 7 through the backports repository


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From sasa.paporovic at fh-bielefeld.de  Sat May  4 15:03:58 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Sat, 04 May 2013 21:03:58 +0200
Subject: [Bio-Linux] Mail4: How to get it now?
Message-ID: <29675_1367694239_ZZi0m2jzpQBmr.00_fc60a6667823.518577be@fh-bielefeld.de>

To 4: ?How to get it now??

Simple, it is like with every other software, because the backports repositories is enabled in Ubuntu12.04/Biolinux 7 by default.
On one hand you can use Software-Center to find it and install it.
(Sometimes the search functionality of Software-Center is not working properly. If you feel the same you may give it a ?Also affects me?(left upper corner) at:

https://bugs.launchpad.net/ubuntu/+source/software-center/+bug/1025237

[Please, a comment is not needed and a little bit contraproductive if you tell that you are on a Ubuntu derivative(Biolinux). Core developers have the tendency to stay a bit away form such reports.]

The second method is classic

1.Call a terminal.
2.Run

sudo apt-get update

(Optional)3. After this run

sudo apt-get dist-upgrade

to install the latest upgrades, inclusive kernel series 3.2.x ones.

4.And finally run 

sudo apt-get install concavity

That it is:
-A short introduction to concavity can be gathered from the manpages after installation

You can call this with a terminal and the line

man concavity

-There is also a second information source. A video tutorial from me, which shows the full workflow for concavity.
But, ? shame on me,... I have not get it managed to provide this for free.
Sorry colleagues, but I have the problem to get the magic working that brings the bun from my baker onto my table for breakfeast.

In moment I am still investing for a good platform for uploading. 

The video should be available within the weekend of the next week. A mail will be send arround here, if this is o.K to the policy of this list.




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From sasa.paporovic at fh-bielefeld.de  Sat May  4 15:08:29 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Sat, 04 May 2013 21:08:29 +0200
Subject: [Bio-Linux] Mail5:Can we get more backports for the newest software
 in bioinformatics?
Message-ID: <15496_1367694510_ZZi0m1j3qvFJ2.00_fc70c98b3752.518578cd@fh-bielefeld.de>

To 5:?Can we get more backports for the newest software in bioinformatics??

Yes, and in the same moment: No.

The greatest advance of the backporting process is that it is community driven. The greatest drawback is that it is only community driven.

So, I am not a Jenkins, not a Hudson and the game is called: Get one give two.

There is a mathematical deep laying cause for the name of the game, which can be found in the work of John von Neumann, the founder of game theorie(and many other stuff).

But for short: 

Think of bit torrent and ask: ?What would happen if there are more leachers than seeds?!?

You can vary a bit  with the both parameters here. What you will see immediately is that some configurations will work better than others.

Line under.

What I have for you is an invitation.

I am your guide, I am your scout in the jungle of backportable software, in the genealogy of distributions(Debian, Ubuntu, Biolinux), but the work for a specific backport must be done by you. I show you how it works.

When this is acceptable to you, you may want to send me a private mail to 

melchiaros at aol.com

That is enough for now.


Communication and organization platform for openSource projects are well known and will be used if E-Mail become uncomfortable.

Greetings

melchiaros

(aka Sasa Paporovic)


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From ebm3 at leicester.ac.uk  Tue May  7 10:07:46 2013
From: ebm3 at leicester.ac.uk (Mallon, Eamonn B. (Dr.))
Date: Tue, 7 May 2013 15:07:46 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
Message-ID: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>

Hi
I've just installed biolinux 7. I tried to run top hat through galaxy and I keep getting an error. It seems to be because bowtie2 doesn't exist. Has  anyone had a similar experience. Any tips?

Eamonn


Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester

http://www2.le.ac.uk/departments/biology/people/mallon

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From tbooth at ceh.ac.uk  Tue May  7 10:39:05 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 7 May 2013 15:39:05 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
Message-ID: <1367937545.20970.771.camel@balisaur>

Hi Eamonn,

It seems there is an omission in the update script, so it could well be
that you are missing bowtie2 and you just have bowtie on there.  Please
try:

sudo apt-get install bowtie2 bowtie2-examples

Hopefully this will be enough to get Galaxy working, but please be aware
that the Galaxy configuration is badly in need of maintenance and it may
still not work.  If so, please send the full error message and I'll see
what I can do.

Cheers,

TIM

On Tue, 2013-05-07 at 15:07 +0100, Mallon, Eamonn B. (Dr.) wrote:
> Hi
> I've just installed biolinux 7. I tried to run top hat through galaxy
> and I keep getting an error. It seems to be because bowtie2 doesn't
> exist. Has  anyone had a similar experience. Any tips?
> 
> 
> Eamonn
> 
> 
> 
> 
> Dr Eamonn Mallon
> Lecturer in Evolutionary Biology
> Adrian 220
> Biology Department
> University of Leicester
> 
> 
> http://www2.le.ac.uk/departments/biology/people/mallon
> 
> 

-- 
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 ebm3 at leicester.ac.uk  Wed May  8 02:54:58 2013
From: ebm3 at leicester.ac.uk (Mallon, Eamonn B. (Dr.))
Date: Wed, 8 May 2013 07:54:58 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <1367937545.20970.771.camel@balisaur>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>,
	<1367937545.20970.771.camel@balisaur>
Message-ID: <DEB77C65357E0E459F13EC8BAAB02CBC019F5E447F25@EXC-MBX1.cfs.le.ac.uk>

Hi Tim,
I really appreciate you getting back to me so quickly and generally for all the work you've done on BioLinux.

I tried your suggestion. Bowtie2 now works but neither tophat nor tophat2 do. See error report below. Version 2.1.0 of bowtie2 is installed

Thanks
Eamonn


Dataset 73: Tophat2 on data 4 and data 6: deletions
Tool execution generated the following error message:

Error in tophat:

[2013-05-08 07:47:45] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-05-08 07:47:45] Checking for Bowtie
Error: TopHat requires Bowtie 2.0.5 or later

The tool produced the following additional output:

Settings:
  Output files: "/tmp/tmphaTcDz/dataset_6.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /usr/lib/galaxy-server/database/files/000/dataset_6.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 12804
Using parameters --bmax 9603 --dcv 1024
  Doing ahead-of-time memory usage test
TopHat v2.0.7
  Passed!  Constructing with these parameters: --bmax 9603 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 1; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 6401.5 (target: 9602)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 7826
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 7827
Getting block 2 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 8958
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 8959
Getting block 3 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 926
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 927
Getting block 4 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 9019
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 9020
Getting block 5 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 9538
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 9539
Getting block 6 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 1983
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1984
Getting block 7 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 7919
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 7920
Getting block 8 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 5043
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 5044
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 12811
fchr[G]: 25322
fchr[T]: 37448
fchr[$]: 51219
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.1.bt2
Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 51219
    bwtLen: 51220
    sz: 12805
    bwtSz: 12805
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3202
    offsSz: 12808
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 267
    numLines: 267
    ebwtTotLen: 17088
    ebwtTotSz: 17088
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 12804
Using parameters --bmax 9603 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 9603 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 1; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 6401.5 (target: 9602)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 7682
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 7683
Getting block 2 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 6747
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 6748
Getting block 3 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 4689
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 4690
Getting block 4 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 7452
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 7453
Getting block 5 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 6415
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 6416
Getting block 6 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 7731
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 7732
Getting block 7 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 8264
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 8265
Getting block 8 of 8
  Reserving size (9603) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:00
  Sorting block of length 2232
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 2233
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 12811
fchr[G]: 25322
fchr[T]: 37448
fchr[$]: 51219
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.1.bt2
Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 51219
    bwtLen: 51220
    sz: 12805
    bwtSz: 12805
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3202
    offsSz: 12808
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 267
    numLines: 267
    ebwtTotLen: 17088
    ebwtTotSz: 17088
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00
tophat2 -p 4  /tmp/tmphaTcDz/dataset_6 /usr/lib/galaxy-server/database/files/000/dataset_4.dat

________________________________________
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: Tuesday, May 07, 2013 3:39 PM
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Bowtie 2 and Galaxy

Hi Eamonn,

It seems there is an omission in the update script, so it could well be
that you are missing bowtie2 and you just have bowtie on there.  Please
try:

sudo apt-get install bowtie2 bowtie2-examples

Hopefully this will be enough to get Galaxy working, but please be aware
that the Galaxy configuration is badly in need of maintenance and it may
still not work.  If so, please send the full error message and I'll see
what I can do.

Cheers,

TIM

On Tue, 2013-05-07 at 15:07 +0100, Mallon, Eamonn B. (Dr.) wrote:
> Hi
> I've just installed biolinux 7. I tried to run top hat through galaxy
> and I keep getting an error. It seems to be because bowtie2 doesn't
> exist. Has  anyone had a similar experience. Any tips?
>
>
> Eamonn
>
>
>
>
> Dr Eamonn Mallon
> Lecturer in Evolutionary Biology
> Adrian 220
> Biology Department
> University of Leicester
>
>
> http://www2.le.ac.uk/departments/biology/people/mallon
>
>

--
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  Wed May  8 04:54:25 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 8 May 2013 09:54:25 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <DEB77C65357E0E459F13EC8BAAB02CBC019F5E447F25@EXC-MBX1.cfs.le.ac.uk>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	, <1367937545.20970.771.camel@balisaur>
	<DEB77C65357E0E459F13EC8BAAB02CBC019F5E447F25@EXC-MBX1.cfs.le.ac.uk>
Message-ID: <1368003265.20970.779.camel@balisaur>

Hi Eamonn,

Oh dear - I just tried running the basic example/test dataset on tophat2
via the command line on my machine and I got the same error, so the
installation is totally broken. I'm not sure which update caused that
(it worked before - honest!) but hopefully it will be a simple fix.
I'll look into it right now.

Cheers,

TIM

On Wed, 2013-05-08 at 07:54 +0100, Mallon, Eamonn B. (Dr.) wrote:
> Hi Tim,
> I really appreciate you getting back to me so quickly and generally
> for all the work you've done on BioLinux.
> 
> I tried your suggestion. Bowtie2 now works but neither tophat nor
> tophat2 do. See error report below. Version 2.1.0 of bowtie2 is
> installed
> 
> Thanks
> Eamonn
> 
> 
> Dataset 73: Tophat2 on data 4 and data 6: deletions
> Tool execution generated the following error message:
> 
> Error in tophat:
> 
> [2013-05-08 07:47:45] Beginning TopHat run (v2.0.7)
> -----------------------------------------------
> [2013-05-08 07:47:45] Checking for Bowtie
> Error: TopHat requires Bowtie 2.0.5 or later
> 
> The tool produced the following additional output:
> 
> Settings:
>   Output files: "/tmp/tmphaTcDz/dataset_6.*.bt2"
>   Line rate: 6 (line is 64 bytes)
>   Lines per side: 1 (side is 64 bytes)
>   Offset rate: 4 (one in 16)
>   FTable chars: 10
>   Strings: unpacked
>   Max bucket size: default
>   Max bucket size, sqrt multiplier: default
>   Max bucket size, len divisor: 4
>   Difference-cover sample period: 1024
>   Endianness: little
>   Actual local endianness: little
>   Sanity checking: disabled
>   Assertions: disabled
>   Random seed: 0
>   Sizeofs: void*:8, int:4, long:8, size_t:8
> Input files DNA, FASTA:
>   /usr/lib/galaxy-server/database/files/000/dataset_6.dat
> Reading reference sizes
>   Time reading reference sizes: 00:00:00
> Calculating joined length
> Writing header
> Reserving space for joined string
> Joining reference sequences
>   Time to join reference sequences: 00:00:00
> bmax according to bmaxDivN setting: 12804
> Using parameters --bmax 9603 --dcv 1024
>   Doing ahead-of-time memory usage test
> TopHat v2.0.7
>   Passed!  Constructing with these parameters: --bmax 9603 --dcv 1024
> Constructing suffix-array element generator
> Building DifferenceCoverSample
>   Building sPrime
>   Building sPrimeOrder
>   V-Sorting samples
>   V-Sorting samples time: 00:00:00
>   Allocating rank array
>   Ranking v-sort output
>   Ranking v-sort output time: 00:00:00
>   Invoking Larsson-Sadakane on ranks
>   Invoking Larsson-Sadakane on ranks time: 00:00:00
>   Sanity-checking and returning
> Building samples
> Reserving space for 12 sample suffixes
> Generating random suffixes
> QSorting 12 sample offsets, eliminating duplicates
> QSorting sample offsets, eliminating duplicates time: 00:00:00
> Multikey QSorting 12 samples
>   (Using difference cover)
>   Multikey QSorting samples time: 00:00:00
> Calculating bucket sizes
>   Binary sorting into buckets
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Binary sorting into buckets time: 00:00:00
> Splitting and merging
>   Splitting and merging time: 00:00:00
> Split 2, merged 7; iterating...
>   Binary sorting into buckets
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Binary sorting into buckets time: 00:00:00
> Splitting and merging
>   Splitting and merging time: 00:00:00
> Split 2, merged 1; iterating...
>   Binary sorting into buckets
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Binary sorting into buckets time: 00:00:00
> Splitting and merging
>   Splitting and merging time: 00:00:00
> Avg bucket size: 6401.5 (target: 9602)
> Converting suffix-array elements to index image
> Allocating ftab, absorbFtab
> Entering Ebwt loop
> Getting block 1 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 7826
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 7827
> Getting block 2 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 8958
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 8959
> Getting block 3 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 926
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 927
> Getting block 4 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 9019
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 9020
> Getting block 5 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 9538
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 9539
> Getting block 6 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 1983
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 1984
> Getting block 7 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 7919
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 7920
> Getting block 8 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 5043
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 5044
> Exited Ebwt loop
> fchr[A]: 0
> fchr[C]: 12811
> fchr[G]: 25322
> fchr[T]: 37448
> fchr[$]: 51219
> Exiting Ebwt::buildToDisk()
> Returning from initFromVector
> Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.1.bt2
> Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.2.bt2
> Re-opening _in1 and _in2 as input streams
> Returning from Ebwt constructor
> Headers:
>     len: 51219
>     bwtLen: 51220
>     sz: 12805
>     bwtSz: 12805
>     lineRate: 6
>     offRate: 4
>     offMask: 0xfffffff0
>     ftabChars: 10
>     eftabLen: 20
>     eftabSz: 80
>     ftabLen: 1048577
>     ftabSz: 4194308
>     offsLen: 3202
>     offsSz: 12808
>     lineSz: 64
>     sideSz: 64
>     sideBwtSz: 48
>     sideBwtLen: 192
>     numSides: 267
>     numLines: 267
>     ebwtTotLen: 17088
>     ebwtTotSz: 17088
>     color: 0
>     reverse: 0
> Total time for call to driver() for forward index: 00:00:00
> Reading reference sizes
>   Time reading reference sizes: 00:00:00
> Calculating joined length
> Writing header
> Reserving space for joined string
> Joining reference sequences
>   Time to join reference sequences: 00:00:00
>   Time to reverse reference sequence: 00:00:00
> bmax according to bmaxDivN setting: 12804
> Using parameters --bmax 9603 --dcv 1024
>   Doing ahead-of-time memory usage test
>   Passed!  Constructing with these parameters: --bmax 9603 --dcv 1024
> Constructing suffix-array element generator
> Building DifferenceCoverSample
>   Building sPrime
>   Building sPrimeOrder
>   V-Sorting samples
>   V-Sorting samples time: 00:00:00
>   Allocating rank array
>   Ranking v-sort output
>   Ranking v-sort output time: 00:00:00
>   Invoking Larsson-Sadakane on ranks
>   Invoking Larsson-Sadakane on ranks time: 00:00:00
>   Sanity-checking and returning
> Building samples
> Reserving space for 12 sample suffixes
> Generating random suffixes
> QSorting 12 sample offsets, eliminating duplicates
> QSorting sample offsets, eliminating duplicates time: 00:00:00
> Multikey QSorting 12 samples
>   (Using difference cover)
>   Multikey QSorting samples time: 00:00:00
> Calculating bucket sizes
>   Binary sorting into buckets
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Binary sorting into buckets time: 00:00:00
> Splitting and merging
>   Splitting and merging time: 00:00:00
> Split 2, merged 7; iterating...
>   Binary sorting into buckets
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Binary sorting into buckets time: 00:00:00
> Splitting and merging
>   Splitting and merging time: 00:00:00
> Split 2, merged 1; iterating...
>   Binary sorting into buckets
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Binary sorting into buckets time: 00:00:00
> Splitting and merging
>   Splitting and merging time: 00:00:00
> Avg bucket size: 6401.5 (target: 9602)
> Converting suffix-array elements to index image
> Allocating ftab, absorbFtab
> Entering Ebwt loop
> Getting block 1 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 7682
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 7683
> Getting block 2 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 6747
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 6748
> Getting block 3 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 4689
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 4690
> Getting block 4 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 7452
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 7453
> Getting block 5 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 6415
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 6416
> Getting block 6 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 7731
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 7732
> Getting block 7 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 8264
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 8265
> Getting block 8 of 8
>   Reserving size (9603) for bucket
>   Calculating Z arrays
>   Calculating Z arrays time: 00:00:00
>   Entering block accumulator loop:
>   10%
>   20%
>   30%
>   40%
>   50%
>   60%
>   70%
>   80%
>   90%
>   100%
>   Block accumulator loop time: 00:00:00
>   Sorting block of length 2232
>   (Using difference cover)
>   Sorting block time: 00:00:00
> Returning block of 2233
> Exited Ebwt loop
> fchr[A]: 0
> fchr[C]: 12811
> fchr[G]: 25322
> fchr[T]: 37448
> fchr[$]: 51219
> Exiting Ebwt::buildToDisk()
> Returning from initFromVector
> Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.1.bt2
> Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.2.bt2
> Re-opening _in1 and _in2 as input streams
> Returning from Ebwt constructor
> Headers:
>     len: 51219
>     bwtLen: 51220
>     sz: 12805
>     bwtSz: 12805
>     lineRate: 6
>     offRate: 4
>     offMask: 0xfffffff0
>     ftabChars: 10
>     eftabLen: 20
>     eftabSz: 80
>     ftabLen: 1048577
>     ftabSz: 4194308
>     offsLen: 3202
>     offsSz: 12808
>     lineSz: 64
>     sideSz: 64
>     sideBwtSz: 48
>     sideBwtLen: 192
>     numSides: 267
>     numLines: 267
>     ebwtTotLen: 17088
>     ebwtTotSz: 17088
>     color: 0
>     reverse: 1
> Total time for backward call to driver() for mirror index: 00:00:00
> tophat2 -p 4  /tmp/tmphaTcDz/dataset_6 /usr/lib/galaxy-server/database/files/000/dataset_4.dat
> 
> ________________________________________
> 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: Tuesday, May 07, 2013 3:39 PM
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] Bowtie 2 and Galaxy
> 
> Hi Eamonn,
> 
> It seems there is an omission in the update script, so it could well be
> that you are missing bowtie2 and you just have bowtie on there.  Please
> try:
> 
> sudo apt-get install bowtie2 bowtie2-examples
> 
> Hopefully this will be enough to get Galaxy working, but please be aware
> that the Galaxy configuration is badly in need of maintenance and it may
> still not work.  If so, please send the full error message and I'll see
> what I can do.
> 
> Cheers,
> 
> TIM
> 
> On Tue, 2013-05-07 at 15:07 +0100, Mallon, Eamonn B. (Dr.) wrote:
> > Hi
> > I've just installed biolinux 7. I tried to run top hat through galaxy
> > and I keep getting an error. It seems to be because bowtie2 doesn't
> > exist. Has  anyone had a similar experience. Any tips?
> >
> >
> > Eamonn
> >
> >
> >
> >
> > Dr Eamonn Mallon
> > Lecturer in Evolutionary Biology
> > Adrian 220
> > Biology Department
> > University of Leicester
> >
> >
> > http://www2.le.ac.uk/departments/biology/people/mallon
> >
> >
> 
> --
> 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
> _______________________________________________
> 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 ebm3 at leicester.ac.uk  Wed May  8 04:56:20 2013
From: ebm3 at leicester.ac.uk (Mallon, Eamonn B. (Dr.))
Date: Wed, 8 May 2013 09:56:20 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <1368003265.20970.779.camel@balisaur>
Message-ID: <CDAFD1A3.A719%ebm3@mail.cfs.le.ac.uk>

I found this on the top hat webpage


          TopHat 2.0.8 release 2/26/2013
          Note (4/12/2013): patched version 2.0.8b was released in order to
provide compatibility with Bowtie v1.0.0
           Version 2.0.8 is a quick fix release addressing the following issues:


*  This version correctly handles the newest version of Bowtie2 v2.1.0.


*  The segment mapping slow-down introduced by some Bowtie2 parameter
changes in version 2.0.7 is now corrected.





Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester

http://www2.le.ac.uk/departments/biology/people/mallon





On 08/05/2013 09:54, "Tim Booth" <tbooth at ceh.ac.uk> wrote:

>Hi Eamonn,
>
>Oh dear - I just tried running the basic example/test dataset on tophat2
>via the command line on my machine and I got the same error, so the
>installation is totally broken. I'm not sure which update caused that
>(it worked before - honest!) but hopefully it will be a simple fix.
>I'll look into it right now.
>
>Cheers,
>
>TIM
>
>On Wed, 2013-05-08 at 07:54 +0100, Mallon, Eamonn B. (Dr.) wrote:
>> Hi Tim,
>> I really appreciate you getting back to me so quickly and generally
>> for all the work you've done on BioLinux.
>>
>> I tried your suggestion. Bowtie2 now works but neither tophat nor
>> tophat2 do. See error report below. Version 2.1.0 of bowtie2 is
>> installed
>>
>> Thanks
>> Eamonn
>>
>>
>> Dataset 73: Tophat2 on data 4 and data 6: deletions
>> Tool execution generated the following error message:
>>
>> Error in tophat:
>>
>> [2013-05-08 07:47:45] Beginning TopHat run (v2.0.7)
>> -----------------------------------------------
>> [2013-05-08 07:47:45] Checking for Bowtie
>> Error: TopHat requires Bowtie 2.0.5 or later
>>
>> The tool produced the following additional output:
>>
>> Settings:
>>   Output files: "/tmp/tmphaTcDz/dataset_6.*.bt2"
>>   Line rate: 6 (line is 64 bytes)
>>   Lines per side: 1 (side is 64 bytes)
>>   Offset rate: 4 (one in 16)
>>   FTable chars: 10
>>   Strings: unpacked
>>   Max bucket size: default
>>   Max bucket size, sqrt multiplier: default
>>   Max bucket size, len divisor: 4
>>   Difference-cover sample period: 1024
>>   Endianness: little
>>   Actual local endianness: little
>>   Sanity checking: disabled
>>   Assertions: disabled
>>   Random seed: 0
>>   Sizeofs: void*:8, int:4, long:8, size_t:8
>> Input files DNA, FASTA:
>>   /usr/lib/galaxy-server/database/files/000/dataset_6.dat
>> Reading reference sizes
>>   Time reading reference sizes: 00:00:00
>> Calculating joined length
>> Writing header
>> Reserving space for joined string
>> Joining reference sequences
>>   Time to join reference sequences: 00:00:00
>> bmax according to bmaxDivN setting: 12804
>> Using parameters --bmax 9603 --dcv 1024
>>   Doing ahead-of-time memory usage test
>> TopHat v2.0.7
>>   Passed!  Constructing with these parameters: --bmax 9603 --dcv 1024
>> Constructing suffix-array element generator
>> Building DifferenceCoverSample
>>   Building sPrime
>>   Building sPrimeOrder
>>   V-Sorting samples
>>   V-Sorting samples time: 00:00:00
>>   Allocating rank array
>>   Ranking v-sort output
>>   Ranking v-sort output time: 00:00:00
>>   Invoking Larsson-Sadakane on ranks
>>   Invoking Larsson-Sadakane on ranks time: 00:00:00
>>   Sanity-checking and returning
>> Building samples
>> Reserving space for 12 sample suffixes
>> Generating random suffixes
>> QSorting 12 sample offsets, eliminating duplicates
>> QSorting sample offsets, eliminating duplicates time: 00:00:00
>> Multikey QSorting 12 samples
>>   (Using difference cover)
>>   Multikey QSorting samples time: 00:00:00
>> Calculating bucket sizes
>>   Binary sorting into buckets
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Binary sorting into buckets time: 00:00:00
>> Splitting and merging
>>   Splitting and merging time: 00:00:00
>> Split 2, merged 7; iterating...
>>   Binary sorting into buckets
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Binary sorting into buckets time: 00:00:00
>> Splitting and merging
>>   Splitting and merging time: 00:00:00
>> Split 2, merged 1; iterating...
>>   Binary sorting into buckets
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Binary sorting into buckets time: 00:00:00
>> Splitting and merging
>>   Splitting and merging time: 00:00:00
>> Avg bucket size: 6401.5 (target: 9602)
>> Converting suffix-array elements to index image
>> Allocating ftab, absorbFtab
>> Entering Ebwt loop
>> Getting block 1 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 7826
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 7827
>> Getting block 2 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 8958
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 8959
>> Getting block 3 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 926
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 927
>> Getting block 4 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 9019
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 9020
>> Getting block 5 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 9538
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 9539
>> Getting block 6 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 1983
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 1984
>> Getting block 7 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 7919
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 7920
>> Getting block 8 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 5043
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 5044
>> Exited Ebwt loop
>> fchr[A]: 0
>> fchr[C]: 12811
>> fchr[G]: 25322
>> fchr[T]: 37448
>> fchr[$]: 51219
>> Exiting Ebwt::buildToDisk()
>> Returning from initFromVector
>> Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.1.bt2
>> Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.2.bt2
>> Re-opening _in1 and _in2 as input streams
>> Returning from Ebwt constructor
>> Headers:
>>     len: 51219
>>     bwtLen: 51220
>>     sz: 12805
>>     bwtSz: 12805
>>     lineRate: 6
>>     offRate: 4
>>     offMask: 0xfffffff0
>>     ftabChars: 10
>>     eftabLen: 20
>>     eftabSz: 80
>>     ftabLen: 1048577
>>     ftabSz: 4194308
>>     offsLen: 3202
>>     offsSz: 12808
>>     lineSz: 64
>>     sideSz: 64
>>     sideBwtSz: 48
>>     sideBwtLen: 192
>>     numSides: 267
>>     numLines: 267
>>     ebwtTotLen: 17088
>>     ebwtTotSz: 17088
>>     color: 0
>>     reverse: 0
>> Total time for call to driver() for forward index: 00:00:00
>> Reading reference sizes
>>   Time reading reference sizes: 00:00:00
>> Calculating joined length
>> Writing header
>> Reserving space for joined string
>> Joining reference sequences
>>   Time to join reference sequences: 00:00:00
>>   Time to reverse reference sequence: 00:00:00
>> bmax according to bmaxDivN setting: 12804
>> Using parameters --bmax 9603 --dcv 1024
>>   Doing ahead-of-time memory usage test
>>   Passed!  Constructing with these parameters: --bmax 9603 --dcv 1024
>> Constructing suffix-array element generator
>> Building DifferenceCoverSample
>>   Building sPrime
>>   Building sPrimeOrder
>>   V-Sorting samples
>>   V-Sorting samples time: 00:00:00
>>   Allocating rank array
>>   Ranking v-sort output
>>   Ranking v-sort output time: 00:00:00
>>   Invoking Larsson-Sadakane on ranks
>>   Invoking Larsson-Sadakane on ranks time: 00:00:00
>>   Sanity-checking and returning
>> Building samples
>> Reserving space for 12 sample suffixes
>> Generating random suffixes
>> QSorting 12 sample offsets, eliminating duplicates
>> QSorting sample offsets, eliminating duplicates time: 00:00:00
>> Multikey QSorting 12 samples
>>   (Using difference cover)
>>   Multikey QSorting samples time: 00:00:00
>> Calculating bucket sizes
>>   Binary sorting into buckets
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Binary sorting into buckets time: 00:00:00
>> Splitting and merging
>>   Splitting and merging time: 00:00:00
>> Split 2, merged 7; iterating...
>>   Binary sorting into buckets
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Binary sorting into buckets time: 00:00:00
>> Splitting and merging
>>   Splitting and merging time: 00:00:00
>> Split 2, merged 1; iterating...
>>   Binary sorting into buckets
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Binary sorting into buckets time: 00:00:00
>> Splitting and merging
>>   Splitting and merging time: 00:00:00
>> Avg bucket size: 6401.5 (target: 9602)
>> Converting suffix-array elements to index image
>> Allocating ftab, absorbFtab
>> Entering Ebwt loop
>> Getting block 1 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 7682
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 7683
>> Getting block 2 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 6747
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 6748
>> Getting block 3 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 4689
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 4690
>> Getting block 4 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 7452
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 7453
>> Getting block 5 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 6415
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 6416
>> Getting block 6 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 7731
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 7732
>> Getting block 7 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 8264
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 8265
>> Getting block 8 of 8
>>   Reserving size (9603) for bucket
>>   Calculating Z arrays
>>   Calculating Z arrays time: 00:00:00
>>   Entering block accumulator loop:
>>   10%
>>   20%
>>   30%
>>   40%
>>   50%
>>   60%
>>   70%
>>   80%
>>   90%
>>   100%
>>   Block accumulator loop time: 00:00:00
>>   Sorting block of length 2232
>>   (Using difference cover)
>>   Sorting block time: 00:00:00
>> Returning block of 2233
>> Exited Ebwt loop
>> fchr[A]: 0
>> fchr[C]: 12811
>> fchr[G]: 25322
>> fchr[T]: 37448
>> fchr[$]: 51219
>> Exiting Ebwt::buildToDisk()
>> Returning from initFromVector
>> Wrote 4211664 bytes to primary EBWT file:
>>/tmp/tmphaTcDz/dataset_6.rev.1.bt2
>> Wrote 12812 bytes to secondary EBWT file:
>>/tmp/tmphaTcDz/dataset_6.rev.2.bt2
>> Re-opening _in1 and _in2 as input streams
>> Returning from Ebwt constructor
>> Headers:
>>     len: 51219
>>     bwtLen: 51220
>>     sz: 12805
>>     bwtSz: 12805
>>     lineRate: 6
>>     offRate: 4
>>     offMask: 0xfffffff0
>>     ftabChars: 10
>>     eftabLen: 20
>>     eftabSz: 80
>>     ftabLen: 1048577
>>     ftabSz: 4194308
>>     offsLen: 3202
>>     offsSz: 12808
>>     lineSz: 64
>>     sideSz: 64
>>     sideBwtSz: 48
>>     sideBwtLen: 192
>>     numSides: 267
>>     numLines: 267
>>     ebwtTotLen: 17088
>>     ebwtTotSz: 17088
>>     color: 0
>>     reverse: 1
>> Total time for backward call to driver() for mirror index: 00:00:00
>> tophat2 -p 4  /tmp/tmphaTcDz/dataset_6
>>/usr/lib/galaxy-server/database/files/000/dataset_4.dat
>>
>> ________________________________________
>> 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: Tuesday, May 07, 2013 3:39 PM
>> To: Bio-Linux help and discussion
>> Subject: Re: [Bio-Linux] Bowtie 2 and Galaxy
>>
>> Hi Eamonn,
>>
>> It seems there is an omission in the update script, so it could well be
>> that you are missing bowtie2 and you just have bowtie on there.  Please
>> try:
>>
>> sudo apt-get install bowtie2 bowtie2-examples
>>
>> Hopefully this will be enough to get Galaxy working, but please be aware
>> that the Galaxy configuration is badly in need of maintenance and it may
>> still not work.  If so, please send the full error message and I'll see
>> what I can do.
>>
>> Cheers,
>>
>> TIM
>>
>> On Tue, 2013-05-07 at 15:07 +0100, Mallon, Eamonn B. (Dr.) wrote:
>> > Hi
>> > I've just installed biolinux 7. I tried to run top hat through galaxy
>> > and I keep getting an error. It seems to be because bowtie2 doesn't
>> > exist. Has  anyone had a similar experience. Any tips?
>> >
>> >
>> > Eamonn
>> >
>> >
>> >
>> >
>> > Dr Eamonn Mallon
>> > Lecturer in Evolutionary Biology
>> > Adrian 220
>> > Biology Department
>> > University of Leicester
>> >
>> >
>> > http://www2.le.ac.uk/departments/biology/people/mallon
>> >
>> >
>>
>> --
>> 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
>> _______________________________________________
>> 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  Wed May  8 05:50:35 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 8 May 2013 10:50:35 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <CDAFD1A3.A719%ebm3@mail.cfs.le.ac.uk>
References: <CDAFD1A3.A719%ebm3@mail.cfs.le.ac.uk>
Message-ID: <1368006635.20970.782.camel@balisaur>

Yes, that explains it.  I've pushed the new package onto Launchpad and
the update should appear in the update manager for you within the next
hour or so.

https://launchpad.net/~nebc/+archive/bio-linux/+build/4559662

Cheers,

TIM

On Wed, 2013-05-08 at 09:56 +0100, Mallon, Eamonn B. (Dr.) wrote:
> I found this on the top hat webpage
> 
> 
>           TopHat 2.0.8 release 2/26/2013
>           Note (4/12/2013): patched version 2.0.8b was released in order to
> provide compatibility with Bowtie v1.0.0
>            Version 2.0.8 is a quick fix release addressing the following issues:
> 
> 
> *  This version correctly handles the newest version of Bowtie2 v2.1.0.
> 
> 
> *  The segment mapping slow-down introduced by some Bowtie2 parameter
> changes in version 2.0.7 is now corrected.
> 



From ebm3 at leicester.ac.uk  Wed May  8 06:01:52 2013
From: ebm3 at leicester.ac.uk (Mallon, Eamonn B. (Dr.))
Date: Wed, 8 May 2013 11:01:52 +0100
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <1368006635.20970.782.camel@balisaur>
Message-ID: <CDAFE10D.A725%ebm3@mail.cfs.le.ac.uk>

Brilliant Thanks Tim

Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester

http://www2.le.ac.uk/departments/biology/people/mallon





On 08/05/2013 10:50, "Tim Booth" <tbooth at ceh.ac.uk> wrote:

>Yes, that explains it.  I've pushed the new package onto Launchpad and
>the update should appear in the update manager for you within the next
>hour or so.
>
>https://launchpad.net/~nebc/+archive/bio-linux/+build/4559662
>
>Cheers,
>
>TIM
>
>On Wed, 2013-05-08 at 09:56 +0100, Mallon, Eamonn B. (Dr.) wrote:
>> I found this on the top hat webpage
>> 
>> 
>>           TopHat 2.0.8 release 2/26/2013
>>           Note (4/12/2013): patched version 2.0.8b was released in
>>order to
>> provide compatibility with Bowtie v1.0.0
>>            Version 2.0.8 is a quick fix release addressing the
>>following issues:
>> 
>> 
>> *  This version correctly handles the newest version of Bowtie2 v2.1.0.
>> 
>> 
>> *  The segment mapping slow-down introduced by some Bowtie2 parameter
>> changes in version 2.0.7 is now corrected.
>> 
>
>_______________________________________________
>Bio-Linux mailing list
>Bio-Linux at nebclists.nerc.ac.uk
>http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux



From tauqeer9 at gmail.com  Tue May 21 11:48:27 2013
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Tue, 21 May 2013 11:48:27 -0400
Subject: [Bio-Linux] Bowtie 2 and Galaxy
In-Reply-To: <1367937545.20970.771.camel@balisaur>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
Message-ID: <CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>

Hi Tim
I have BioLinux installed on my iMac through Parallels Virtual Machine.
Everything was working absolutely fine until today. This morning, I ran
update manager (from the left side panel) and now I do not see my side and
tope panel. I just see my desktop, nothing else.

Please help

Tauqeer
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From tbooth at ceh.ac.uk  Tue May 21 12:10:10 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 21 May 2013 17:10:10 +0100
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
Message-ID: <1369152610.5211.6.camel@balisaur>

Hi Tauqeer,

That's not good!  First thing is to see if you can get a fallback
desktop.  It's not really a fix but you will at least be able to use
your Bio-Linux system.

If you restart the Parallels VM, I assume you still see the login
manager where it asks for your password?  If you click the icon next to
your name and choose "Gnome desktop (no effects)" can you log in and see
an old-style menu bar and apps menu at the top?

I'd like to see if the update process failed somehow and left the system
in an inconsistent state.  If you can get to the command line, can you
run:

sudo apt-get dist-upgrade

What does it say?

And finally, what happens if you then run:

unity --replace

Cheers,

TIM

On Tue, 2013-05-21 at 16:48 +0100, Tauqeer Alam wrote:
> Hi Tim
> I have BioLinux installed on my iMac through Parallels Virtual
> Machine. Everything was working absolutely fine until today. This
> morning, I ran update manager (from the left side panel) and now I do
> not see my side and tope panel. I just see my desktop, nothing else.
> 
> 
> Please help
> 
> 
> Tauqeer

-- 
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 tauqeer9 at gmail.com  Tue May 21 12:24:41 2013
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Tue, 21 May 2013 12:24:41 -0400
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <1369152610.5211.6.camel@balisaur>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
Message-ID: <CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>

If you restart the Parallels VM, I assume you still see the login
manager where it asks for your password?  If you click the icon next to
your name and choose "Gnome desktop (no effects)" can you log in and see
an old-style menu bar and apps menu at the top?

Yes, at the top left I see "Applications" and "Places". I t has everything
there.

sumiti at ubuntu:~$ sudo apt-get dist-upgrade

[sudo] password for sumiti:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

sumiti at ubuntu:~$ unity --replace

unity-panel-service: no process found
Checking if settings need to be migrated ...no
Checking if internal files need to be migrated ...no
Backend     : gconf
Integration : true
Profile     : unity
Adding plugins
Initializing core options...done
Initializing composite options...done
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libopengl.so'
: libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'opengl'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libcompiztoolbox.so' : libGL.so.1: cannot open shared
object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'compiztoolbox'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libdecor.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'decor'
Initializing vpswitch options...done
Initializing snap options...done
Initializing mousepoll options...done
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libresize.so'
: libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'resize'
Initializing place options...done
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libmove.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'move'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libwall.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'wall'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libgrid.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'grid'
Initializing session options...done
Initializing gnomecompat options...done
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libanimation.so' : libGL.so.1: cannot open shared object
file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'animation'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libfade.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'fade'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libunitymtgrabhandles.so' : libGL.so.1: cannot open shared
object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'unitymtgrabhandles'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libworkarounds.so' : libGL.so.1: cannot open shared object
file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'workarounds'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libscale.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'scale'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libexpo.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'expo'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libezoom.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'ezoom'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libunityshell.so' : libGL.so.1: cannot open shared object
file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'unityshell'
Setting Update "main_menu_key"
Setting Update "run_key"

window is stuck here

Thanks

Tauqeer

On Tue, May 21, 2013 at 12:10 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Tauqeer,
>
> That's not good!  First thing is to see if you can get a fallback
> desktop.  It's not really a fix but you will at least be able to use
> your Bio-Linux system.
>
> If you restart the Parallels VM, I assume you still see the login
> manager where it asks for your password?  If you click the icon next to
> your name and choose "Gnome desktop (no effects)" can you log in and see
> an old-style menu bar and apps menu at the top?
>
> I'd like to see if the update process failed somehow and left the system
> in an inconsistent state.  If you can get to the command line, can you
> run:
>
> sudo apt-get dist-upgrade
>
> What does it say?
>
> And finally, what happens if you then run:
>
> unity --replace
>
> Cheers,
>
> TIM
>
> On Tue, 2013-05-21 at 16:48 +0100, Tauqeer Alam wrote:
> > Hi Tim
> > I have BioLinux installed on my iMac through Parallels Virtual
> > Machine. Everything was working absolutely fine until today. This
> > morning, I ran update manager (from the left side panel) and now I do
> > not see my side and tope panel. I just see my desktop, nothing else.
> >
> >
> > Please help
> >
> >
> > Tauqeer
>
> --
> 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
>



-- 
*********************************************
Md Tauqeer Alam, Ph.D
Division of Infectious Diseases
Emory University School of Medicine
615 Michael Street, Atlanta, GA 30322, USA
tauqeer9 at gmail.com
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From tbooth at ceh.ac.uk  Tue May 21 13:11:55 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 21 May 2013 18:11:55 +0100
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
	<CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
Message-ID: <1369156315.3094.21.camel@balisaur>

Hi,

> compiz (core) - Error: Couldn't load plugin
> '/usr/lib/compiz/libopengl.so' : libGL.so.1: cannot open shared object
> file: No such file or directory

OK, I don't know why this has happened on your system but the error
above appears to be the root cause.  The libGL.so.1 is a shared library
file needed by the Unity desktop.  On my machine it's found at:

/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1

And is owned by the package libgl1-mesa-glx (as revealed by dpkg -S).
Could you please do:

dpkg -l '*libgl1*'

I get a report like the one below.  All the "un" lines are virtual
packages and are not relevant.  Does libgl1-mesa-glx show up as being
installed on your system?  What if you try to install/reinstall it?

sudo apt-get install --reinstall libgl1-mesa-glx

Does that put the file back?

Cheers,

TIM

Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                     Version                  Description
+++-========================-========================-================================================================
un  libgl1                   <none>                   (no description available)
ii  libgl1-mesa-dev          8.0.4-0ubuntu0.5         free implementation of the OpenGL API -- GLX development files
un  libgl1-mesa-dev-lts-quan <none>                   (no description available)
un  libgl1-mesa-dev-lts-rari <none>                   (no description available)
ii  libgl1-mesa-dri          8.0.4-0ubuntu0.5         free implementation of the OpenGL API -- DRI modules
un  libgl1-mesa-dri-dev      <none>                   (no description available)
un  libgl1-mesa-dri-experime <none>                   (no description available)
ii  libgl1-mesa-glx          8.0.4-0ubuntu0.5         free implementation of the OpenGL API -- GLX runtime
un  libgl1-mesa-glx-lts-quan <none>                   (no description available)
un  libgl1-mesa-glx-lts-rari <none>                   (no description available)
un  libgl1-mesa-glx-no-multi <none>                   (no description available)
un  libgl1-mesa-swx11-dev    <none>                   (no description available)
un  libgl1-nvidia-alternativ <none>                   (no description available)


From tauqeer9 at gmail.com  Tue May 21 13:28:13 2013
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Tue, 21 May 2013 13:28:13 -0400
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <1369156315.3094.21.camel@balisaur>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
	<CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
	<1369156315.3094.21.camel@balisaur>
Message-ID: <CAFaE85DidBq46U00pk92apbEcVarwPCHXh4LR+XKwurGcNrX+Q@mail.gmail.com>

Here it is-

sumiti at ubuntu:~$ dpkg -l '*libgl1*'

Desired=Unknown/Install/Remove/Purge/Hold
|
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                     Version                  Description
+++-========================-========================-================================================================
un  libgl1                   <none>                   (no description
available)
ii  libgl1-mesa-dev          8.0.4-0ubuntu0.5         free implementation
of the OpenGL API -- GLX development files
un  libgl1-mesa-dev-lts-quan <none>                   (no description
available)
un  libgl1-mesa-dev-lts-rari <none>                   (no description
available)
ii  libgl1-mesa-dri          8.0.4-0ubuntu0.5         free implementation
of the OpenGL API -- DRI modules
un  libgl1-mesa-dri-dev      <none>                   (no description
available)
un  libgl1-mesa-dri-experime <none>                   (no description
available)
ii  libgl1-mesa-glx          8.0.4-0ubuntu0.5         free implementation
of the OpenGL API -- GLX runtime
un  libgl1-mesa-glx-lts-quan <none>                   (no description
available)
un  libgl1-mesa-glx-lts-rari <none>                   (no description
available)
un  libgl1-mesa-glx-no-multi <none>                   (no description
available)
un  libgl1-mesa-swx11-dev    <none>                   (no description
available)
un  libgl1-nvidia-alternativ <none>                   (no description
available)

sumiti at ubuntu:~$ sudo apt-get install --reinstall libgl1-mesa-glx

sudo] password for sumiti:

Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer
required:
  sbsigntool linux-headers-3.2.0-39-generic linux-headers-3.2.0-37
linux-headers-3.2.0-39
  linux-headers-3.2.0-37-generic language-pack-kde-en kde-l10n-engb
language-pack-kde-en-base
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 2 reinstalled, 0 to remove and 0 not
upgraded.
Need to get 0 B/207 kB of archives.
After this operation, 0 B of additional disk space will be used.
Do you want to continue [Y/n]? Y
(Reading database ... 495926 files and directories currently installed.)
Preparing to replace libgl1-mesa-glx 8.0.4-0ubuntu0.5 (using
.../libgl1-mesa-glx_8.0.4-0ubuntu0.5_amd64.deb) ...
Unpacking replacement libgl1-mesa-glx ...
Preparing to replace libgl1-mesa-glx:i386 8.0.4-0ubuntu0.5 (using
.../libgl1-mesa-glx_8.0.4-0ubuntu0.5_i386.deb) ...
Unpacking replacement libgl1-mesa-glx:i386 ...
Setting up libgl1-mesa-glx (8.0.4-0ubuntu0.5) ...
Setting up libgl1-mesa-glx:i386 (8.0.4-0ubuntu0.5) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
sumiti at ubuntu:~$


Awesome!!!! Everything is back.

THANK YOU VERY MUCH.  BioLinux ROCKS!!

Tauqeer



On Tue, May 21, 2013 at 1:11 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> > compiz (core) - Error: Couldn't load plugin
> > '/usr/lib/compiz/libopengl.so' : libGL.so.1: cannot open shared object
> > file: No such file or directory
>
> OK, I don't know why this has happened on your system but the error
> above appears to be the root cause.  The libGL.so.1 is a shared library
> file needed by the Unity desktop.  On my machine it's found at:
>
> /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1
>
> And is owned by the package libgl1-mesa-glx (as revealed by dpkg -S).
> Could you please do:
>
> dpkg -l '*libgl1*'
>
> I get a report like the one below.  All the "un" lines are virtual
> packages and are not relevant.  Does libgl1-mesa-glx show up as being
> installed on your system?  What if you try to install/reinstall it?
>
> sudo apt-get install --reinstall libgl1-mesa-glx
>
> Does that put the file back?
>
> Cheers,
>
> TIM
>
> Desired=Unknown/Install/Remove/Purge/Hold
> |
> Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name                     Version                  Description
>
> +++-========================-========================-================================================================
> un  libgl1                   <none>                   (no description
> available)
> ii  libgl1-mesa-dev          8.0.4-0ubuntu0.5         free implementation
> of the OpenGL API -- GLX development files
> un  libgl1-mesa-dev-lts-quan <none>                   (no description
> available)
> un  libgl1-mesa-dev-lts-rari <none>                   (no description
> available)
> ii  libgl1-mesa-dri          8.0.4-0ubuntu0.5         free implementation
> of the OpenGL API -- DRI modules
> un  libgl1-mesa-dri-dev      <none>                   (no description
> available)
> un  libgl1-mesa-dri-experime <none>                   (no description
> available)
> ii  libgl1-mesa-glx          8.0.4-0ubuntu0.5         free implementation
> of the OpenGL API -- GLX runtime
> un  libgl1-mesa-glx-lts-quan <none>                   (no description
> available)
> un  libgl1-mesa-glx-lts-rari <none>                   (no description
> available)
> un  libgl1-mesa-glx-no-multi <none>                   (no description
> available)
> un  libgl1-mesa-swx11-dev    <none>                   (no description
> available)
> un  libgl1-nvidia-alternativ <none>                   (no description
> available)
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>



-- 
*********************************************
Md Tauqeer Alam, Ph.D
Division of Infectious Diseases
Emory University School of Medicine
615 Michael Street, Atlanta, GA 30322, USA
tauqeer9 at gmail.com
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From tbooth at ceh.ac.uk  Tue May 21 13:41:30 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 21 May 2013 18:41:30 +0100
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <CAFaE85DidBq46U00pk92apbEcVarwPCHXh4LR+XKwurGcNrX+Q@mail.gmail.com>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
	<CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
	<1369156315.3094.21.camel@balisaur>
	<CAFaE85DidBq46U00pk92apbEcVarwPCHXh4LR+XKwurGcNrX+Q@mail.gmail.com>
Message-ID: <1369158090.3094.27.camel@balisaur>

Hi,

Great to hear it was fixed so easily.  I do wonder why that file might
have vanished in the first place.  Gremlins, I guess. ;-)

Cheers,

TIM




From tauqeer9 at gmail.com  Tue May 21 14:08:22 2013
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Tue, 21 May 2013 14:08:22 -0400
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <1369158090.3094.27.camel@balisaur>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
	<CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
	<1369156315.3094.21.camel@balisaur>
	<CAFaE85DidBq46U00pk92apbEcVarwPCHXh4LR+XKwurGcNrX+Q@mail.gmail.com>
	<1369158090.3094.27.camel@balisaur>
Message-ID: <CAFaE85CpqC_EuiGM0SEvaVCrv+HQJYtGuWAfMh4SfAPDvLWd_g@mail.gmail.com>

Hi Tim
Thank you very much for being so helpful. I am from biology background so I
do not understand too much details about the errors. Most of the time I try
to solve by taking help from Google, but this one was kind of tricky.
I would also like to take this opportunity to ask you another question. Do
you have any plan to add genome annotation tools-such as AGeS (specially
this one), Prokka, MAKER or BG7 in the BioLinux?

Appreciate you help.

Tauqeer



On Tue, May 21, 2013 at 1:41 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> Great to hear it was fixed so easily.  I do wonder why that file might
> have vanished in the first place.  Gremlins, I guess. ;-)
>
> Cheers,
>
> TIM
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>



-- 
*********************************************
Md Tauqeer Alam, Ph.D
Division of Infectious Diseases
Emory University School of Medicine
615 Michael Street, Atlanta, GA 30322, USA
tauqeer9 at gmail.com
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From tbooth at ceh.ac.uk  Wed May 22 09:52:13 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 22 May 2013 14:52:13 +0100
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <CAFaE85CpqC_EuiGM0SEvaVCrv+HQJYtGuWAfMh4SfAPDvLWd_g@mail.gmail.com>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
	<CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
	<1369156315.3094.21.camel@balisaur>
	<CAFaE85DidBq46U00pk92apbEcVarwPCHXh4LR+XKwurGcNrX+Q@mail.gmail.com>
	<1369158090.3094.27.camel@balisaur>
	<CAFaE85CpqC_EuiGM0SEvaVCrv+HQJYtGuWAfMh4SfAPDvLWd_g@mail.gmail.com>
Message-ID: <1369230733.3094.61.camel@balisaur>

Hi Tauqeer,

It would be nice to have some genome annotation tools on Bio-Linux but I
have to prioritise the needs of our supported NERC user community first.
If a pipeline is big and complicated to install, which these are, they
require correspondingly more effort to set up and maintain as packages
so I can't just add them as a quick job.  Their installation
instructions often ask you to set insecure configurations for the web
server or database servers which may be fine for individual users but I
can't apply these to every Bio-Linux installation.  There are also
licensing issues:

For MAKER, the pipeline itself is free but it depends on some components
(ie. TRF) that, according to the license, cannot be redistributed by
third parties.

Prokka also has the same problem.  Unfortunately the people who make the
tools that these "free" pipelines need explicitly don't want these
incorporating onto systems like Bio-Linux and apply licensing conditions
accordingly.

Cheers,

TIM

On Tue, 2013-05-21 at 19:08 +0100, Tauqeer Alam wrote:
> Hi Tim
> Thank you very much for being so helpful. I am from biology background
> so I do not understand too much details about the errors. Most of the
> time I try to solve by taking help from Google, but this one was kind
> of tricky.
> I would also like to take this opportunity to ask you
> another question. Do you have any plan to add genome annotation
> tools-such as AGeS (specially this one), Prokka, MAKER or BG7 in the
> BioLinux?
> 
> 
> Appreciate you help.
> 
> 
> Tauqeer
> 
> 
> 
> 
> On Tue, May 21, 2013 at 1:41 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>         Hi,
>         
>         Great to hear it was fixed so easily.  I do wonder why that
>         file might
>         have vanished in the first place.  Gremlins, I guess. ;-)
>         
>         Cheers,
>         
>         TIM
>         
>         
>         _______________________________________________
>         Bio-Linux mailing list
>         Bio-Linux at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         
> 
> 
> 
> 
> -- 
> *********************************************
> Md Tauqeer Alam, Ph.D
> Division of Infectious Diseases
> Emory University School of Medicine
> 615 Michael Street, Atlanta, GA 30322, USA
> tauqeer9 at gmail.com
> 

-- 
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 tauqeer9 at gmail.com  Wed May 22 11:23:21 2013
From: tauqeer9 at gmail.com (Tauqeer Alam)
Date: Wed, 22 May 2013 11:23:21 -0400
Subject: [Bio-Linux] System on Parallels broken after updates
In-Reply-To: <1369230733.3094.61.camel@balisaur>
References: <CDAEC942.A6B5%ebm3@mail.cfs.le.ac.uk>
	<1367937545.20970.771.camel@balisaur>
	<CAFaE85CMoxUF5EUSPF7W1X8e8cX8ZwJefoJCroPsDg5HtX-2kA@mail.gmail.com>
	<1369152610.5211.6.camel@balisaur>
	<CAFaE85CudMcnUtG3jSDqwftWy87A6zzsvUtV25w6jNDX0jOiTw@mail.gmail.com>
	<1369156315.3094.21.camel@balisaur>
	<CAFaE85DidBq46U00pk92apbEcVarwPCHXh4LR+XKwurGcNrX+Q@mail.gmail.com>
	<1369158090.3094.27.camel@balisaur>
	<CAFaE85CpqC_EuiGM0SEvaVCrv+HQJYtGuWAfMh4SfAPDvLWd_g@mail.gmail.com>
	<1369230733.3094.61.camel@balisaur>
Message-ID: <CAFaE85CEyW0xjV3XZVnAvBC6dto-BbXyhG97iCC+DkejkFUL7g@mail.gmail.com>

Thanks Tim! I understand your point. I will try to install one of them
myself.

Thank you again for all your help.

Tauqeer

On Wed, May 22, 2013 at 9:52 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Tauqeer,
>
> It would be nice to have some genome annotation tools on Bio-Linux but I
> have to prioritise the needs of our supported NERC user community first.
> If a pipeline is big and complicated to install, which these are, they
> require correspondingly more effort to set up and maintain as packages
> so I can't just add them as a quick job.  Their installation
> instructions often ask you to set insecure configurations for the web
> server or database servers which may be fine for individual users but I
> can't apply these to every Bio-Linux installation.  There are also
> licensing issues:
>
> For MAKER, the pipeline itself is free but it depends on some components
> (ie. TRF) that, according to the license, cannot be redistributed by
> third parties.
>
> Prokka also has the same problem.  Unfortunately the people who make the
> tools that these "free" pipelines need explicitly don't want these
> incorporating onto systems like Bio-Linux and apply licensing conditions
> accordingly.
>
> Cheers,
>
> TIM
>
> On Tue, 2013-05-21 at 19:08 +0100, Tauqeer Alam wrote:
> > Hi Tim
> > Thank you very much for being so helpful. I am from biology background
> > so I do not understand too much details about the errors. Most of the
> > time I try to solve by taking help from Google, but this one was kind
> > of tricky.
> > I would also like to take this opportunity to ask you
> > another question. Do you have any plan to add genome annotation
> > tools-such as AGeS (specially this one), Prokka, MAKER or BG7 in the
> > BioLinux?
> >
> >
> > Appreciate you help.
> >
> >
> > Tauqeer
> >
> >
> >
> >
> > On Tue, May 21, 2013 at 1:41 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> >         Hi,
> >
> >         Great to hear it was fixed so easily.  I do wonder why that
> >         file might
> >         have vanished in the first place.  Gremlins, I guess. ;-)
> >
> >         Cheers,
> >
> >         TIM
> >
> >
> >         _______________________________________________
> >         Bio-Linux mailing list
> >         Bio-Linux at nebclists.nerc.ac.uk
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> >
> >
> >
> > --
> > *********************************************
> > Md Tauqeer Alam, Ph.D
> > Division of Infectious Diseases
> > Emory University School of Medicine
> > 615 Michael Street, Atlanta, GA 30322, USA
> > tauqeer9 at gmail.com
> >
>
> --
> 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
>



-- 
*********************************************
Md Tauqeer Alam, Ph.D
Division of Infectious Diseases
Emory University School of Medicine
615 Michael Street, Atlanta, GA 30322, USA
tauqeer9 at gmail.com
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From kissaj at miamioh.edu  Fri May 24 16:43:36 2013
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Fri, 24 May 2013 16:43:36 -0400
Subject: [Bio-Linux] BioLinux install failure
Message-ID: <1369428216.3523.111.camel@methy1>

Hi Tim,

    Just ran into an install failure issue with a DELL T3400
(Workstation).  The live DVD works great.  After install the X server
fails and when I try to install the nvidia drivers, they won't build
because the kernel source package for 3.5.0-26 isn't available and I
can't seem to find it...

    Is there a source package for the linux-source-3.5.0 available?

Thanks,
Andor
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From tbooth at ceh.ac.uk  Tue May 28 06:08:05 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 28 May 2013 11:08:05 +0100
Subject: [Bio-Linux] BioLinux install failure
In-Reply-To: <1369428216.3523.111.camel@methy1>
References: <1369428216.3523.111.camel@methy1>
Message-ID: <1369735685.6820.102.camel@balisaur>

Hi Andor,

I did switch to the 3.5 series (Quantal backported) kernel on the latest
DVD, as this is the one used by Ubuntu 12.04.2 and has improved hardware
compatibility.  (If there are problems with it then you can switch back
to the 3.2 series but I assume this isn't the issue here.)

Please try installing the package:

linux-headers-generic-lts-quantal

Does that fix the NVidia build?  If not, I'll look more closely.

Cheers,

TIM

On Fri, 2013-05-24 at 21:43 +0100, Andor J Kiss wrote:
> Hi Tim,
> 
>     Just ran into an install failure issue with a DELL T3400
> (Workstation).  The live DVD works great.  After install the X server
> fails and when I try to install the nvidia drivers, they won't build
> because the kernel source package for 3.5.0-26 isn't available and I
> can't seem to find it...
> 
>     Is there a source package for the linux-source-3.5.0 available?
> 
> Thanks,
> Andor

-- 
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 kissaj at miamioh.edu  Tue May 28 15:24:57 2013
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Tue, 28 May 2013 15:24:57 -0400
Subject: [Bio-Linux] BioLinux install failure
In-Reply-To: <1369735685.6820.102.camel@balisaur>
References: <1369428216.3523.111.camel@methy1>
	<1369735685.6820.102.camel@balisaur>
Message-ID: <1369769097.3639.96.camel@methy1>

Hi Tim,

    Ok - I'll try that; should work.  I'll let you know if we any
further issues.

    BTW:  I'm handing out 40 BioLinux Live DVDs at the NorthEast Ohio
Bioinformatics Workshop (for undergrads and Grads).

Cheers,
Andor

On Tue, 2013-05-28 at 11:08 +0100, Tim Booth wrote: 

> Hi Andor,
> 
> I did switch to the 3.5 series (Quantal backported) kernel on the latest
> DVD, as this is the one used by Ubuntu 12.04.2 and has improved hardware
> compatibility.  (If there are problems with it then you can switch back
> to the 3.2 series but I assume this isn't the issue here.)
> 
> Please try installing the package:
> 
> linux-headers-generic-lts-quantal
> 
> Does that fix the NVidia build?  If not, I'll look more closely.
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2013-05-24 at 21:43 +0100, Andor J Kiss wrote:
> > Hi Tim,
> > 
> >     Just ran into an install failure issue with a DELL T3400
> > (Workstation).  The live DVD works great.  After install the X server
> > fails and when I try to install the nvidia drivers, they won't build
> > because the kernel source package for 3.5.0-26 isn't available and I
> > can't seem to find it...
> > 
> >     Is there a source package for the linux-source-3.5.0 available?
> > 
> > Thanks,
> > Andor
> 
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From tbooth at ceh.ac.uk  Wed May 29 04:48:19 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 29 May 2013 09:48:19 +0100
Subject: [Bio-Linux] BioLinux install failure
In-Reply-To: <1369769097.3639.96.camel@methy1>
References: <1369428216.3523.111.camel@methy1>
	<1369735685.6820.102.camel@balisaur> <1369769097.3639.96.camel@methy1>
Message-ID: <1369817299.6820.129.camel@balisaur>

Hi Andor,

>     BTW:  I'm handing out 40 BioLinux Live DVDs at the NorthEast Ohio
> Bioinformatics Workshop (for undergrads and Grads).

Wow, that's fantastic to hear.  Must have taken a while to make, or did
you get your hands on a bulk duplicator?  In any case, I hope they find
them useful, and maybe it will bring a few more people to the Bio-Linux
community.

Any time we hear about Bio-Linux being promoted, or used for teaching,
or in a large deployment it's one more bit of ammunition to show that
the project is worthy of continued/increased funding so please do keep
telling us about things like this.

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 kissaj at miamioh.edu  Fri May 31 09:36:40 2013
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Fri, 31 May 2013 09:36:40 -0400
Subject: [Bio-Linux] BioLinux install failure
In-Reply-To: <1369817299.6820.129.camel@balisaur>
References: <1369428216.3523.111.camel@methy1>
	<1369735685.6820.102.camel@balisaur> <1369769097.3639.96.camel@methy1>
	<1369817299.6820.129.camel@balisaur>
Message-ID: <1370007400.17028.86.camel@methy1>

Yep, It did take a while, but I'm finding that for A LOT of people find
that BioLinux is increasingly the ideal solution; especially for the R,
ARB, QIIME, Mothur, and Galaxy installs...all the stuff that most
end-user biologists cannot deal with.

We use it on both our heavy server/workstations for genome assembly
(also running CLC Genomics Workbench).  Plus being a open-access
training facility/centre,  it eliminates the dreaded "I'm going to
insert my USB stick with evil windows viruses to crash this (windows)
bioinformatics computer" issue.

And with about 50% of our users already using MAC OSX, the jump to
BioLinux (Ubuntu) is now really small.

Cheers,
-- 
__________________________________________________________________
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://www.cas.muohio.edu/cbfg 
URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss 




On Wed, 2013-05-29 at 09:48 +0100, Tim Booth wrote: 

> Hi Andor,
> 
> >     BTW:  I'm handing out 40 BioLinux Live DVDs at the NorthEast Ohio
> > Bioinformatics Workshop (for undergrads and Grads).
> 
> Wow, that's fantastic to hear.  Must have taken a while to make, or did
> you get your hands on a bulk duplicator?  In any case, I hope they find
> them useful, and maybe it will bring a few more people to the Bio-Linux
> community.
> 
> Any time we hear about Bio-Linux being promoted, or used for teaching,
> or in a large deployment it's one more bit of ammunition to show that
> the project is worthy of continued/increased funding so please do keep
> telling us about things like this.
> 
> Cheers,
> 
> TIM
> 
> 
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