From sasa.paporovic at fh-bielefeld.de  Mon Sep  2 12:45:35 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Mon, 02 Sep 2013 18:45:35 +0200
Subject: [Bio-Linux] paper aggregation website
In-Reply-To: <7790bfb08d47f.5224c0a8@fh-bielefeld.de>
References: <7720984588604.5224bcaa@fh-bielefeld.de>
	<7450cfbc8ec2d.5224bce7@fh-bielefeld.de>
	<7790bfb08d47f.5224c0a8@fh-bielefeld.de>
Message-ID: <7450f5b089cca.5224dccf@fh-bielefeld.de>

 P { margin-bottom: 0.21cm; }A:link { } 
Hi,

there is a project
called "Cytoscape", which is also included in Biolinux. It
is a multi purposes network analysis/visualization suite, especially
usable for bio-networks of different kind.
 

 
 
On there homepage 
 

 
 
http://www.cytoscape.org/
 

 
 
they are featuring the papers that were
written about Cytoscape or in which Cytoscape was simply used. Not so
much their own papers, even if you can find them also, more the
papers of the scientific community that uses Cytoscape.
 

 
 

 
 
They also link to a tumbler aggregation
page for that papers: 
 

 
 
 http://cytoscape-publications.tumblr.com/
 

 
 
Can you do the same for Biolinux on
your homepage. Maybe it helps you to get some fundings, and it would
be of great benefit to the community to get the papers more in front
of the view.
 

 
 
Greetings
 

 
 
Sasa Paporovic
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From tbooth at ceh.ac.uk  Tue Sep  3 07:03:02 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 3 Sep 2013 12:03:02 +0100
Subject: [Bio-Linux] paper aggregation website
In-Reply-To: <7450f5b089cca.5224dccf@fh-bielefeld.de>
References: <7720984588604.5224bcaa@fh-bielefeld.de>
	<7450cfbc8ec2d.5224bce7@fh-bielefeld.de>
	<7790bfb08d47f.5224c0a8@fh-bielefeld.de>
	<7450f5b089cca.5224dccf@fh-bielefeld.de>
Message-ID: <1378206182.25700.104.camel@balisaur>

Hi,

I agree we really need to put more love into the Bio-Linux site, and a
section on research highlights from Bio-Linux users would be an
excellent feature.  It's just a matter of time priorities at the moment.

It looks like the Cytoscape people are manually curating a list of their
favourite papers, but I wondered if I could do something quickly by
embedding something like a citation feed from PubMed into the Bio-Linux
web page.  I didn't find a good way to do this yet but I'll keep
looking.  In the meantime I've just added a link to Google Scholar which
people can follow:

http://nebc.nerc.ac.uk/tools/bio-linux now links to:

http://scholar.google.co.uk/scholar?hl=en&as_sdt=2005&sciodt=1,5&cites=16561082859102228201&scipsc=&q=&scisbd=1

Cheers,

TIM

On Mon, 2013-09-02 at 17:45 +0100, Sasa Paporovic wrote:
> Hi,
> 
> there is a project called "Cytoscape", which is also included in
> Biolinux. It is a multi purposes network analysis/visualization suite,
> especially usable for bio-networks of different kind.
> 
> 
> On there homepage 
> 
> 
> http://www.cytoscape.org/
> 
> 
> they are featuring the papers that were written about Cytoscape or in
> which Cytoscape was simply used. Not so much their own papers, even if
> you can find them also, more the papers of the scientific community
> that uses Cytoscape.
> 
> 
> 
> They also link to a tumbler aggregation page for that papers: 
> 
> 
> http://cytoscape-publications.tumblr.com/
> 
> 
> Can you do the same for Biolinux on your homepage. Maybe it helps you
> to get some fundings, and it would be of great benefit to the
> community to get the papers more in front of the view.
> 
> 
> Greetings
> 
> 
> Sasa Paporovic
> 

-- 
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  Wed Sep  4 10:17:03 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Wed, 04 Sep 2013 16:17:03 +0200
Subject: [Bio-Linux] license of Bio-Linux artwork in package themes-v7
In-Reply-To: <7780f9a1dc332.522740a5@fh-bielefeld.de>
References: <74c0d7cadc222.52273ac3@fh-bielefeld.de>
	<76f0aad0dc7b0.52273b01@fh-bielefeld.de>
	<74a09f6edd619.52273b3e@fh-bielefeld.de>
	<7480cf6adbae4.52273dd3@fh-bielefeld.de>
	<71b09b29da33c.52273e0f@fh-bielefeld.de>
	<7780f9a1dc332.522740a5@fh-bielefeld.de>
Message-ID: <7620f297ded30.52275cff@fh-bielefeld.de>

 P { margin-bottom: 0.21cm; }A:link { } 
Hi there,

I want to use some
themes/logos/icons of different Linux distributions in a paper.
One of the affected one is Bio-Linux. I have downloaded the theme package
from
 

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

 
 
After an examination with file-roller I
was not able to find any license information either for the package
nor for a single file. EXIF data shows also no license information.
 

 
 
So, just this little mail. I want to
ask if it is possible to get some license information or the simple
permission to use the two .jpg in
 

 
 
/usr/share/backgrounds/
 

 
 
of the package.
 

 
 
The first is the biolinux 5 theme, the
second is a designed one by Marcin Jankowski.
 

 
 
Could you forward if needed?
 

 
 
Thanks
 

 
 
Sasa Paporovic
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From tbooth at ceh.ac.uk  Wed Sep  4 11:45:34 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 4 Sep 2013 16:45:34 +0100
Subject: [Bio-Linux] license of Bio-Linux artwork in package themes-v7
In-Reply-To: <7620f297ded30.52275cff@fh-bielefeld.de>
References: <74c0d7cadc222.52273ac3@fh-bielefeld.de>
	<76f0aad0dc7b0.52273b01@fh-bielefeld.de>
	<74a09f6edd619.52273b3e@fh-bielefeld.de>
	<7480cf6adbae4.52273dd3@fh-bielefeld.de>
	<71b09b29da33c.52273e0f@fh-bielefeld.de>
	<7780f9a1dc332.522740a5@fh-bielefeld.de>
	<7620f297ded30.52275cff@fh-bielefeld.de>
Message-ID: <1378309534.25700.254.camel@balisaur>

Hi Sasa,

Unfortunately I don't have specific license information for these files
but here's what I know:

The Bio-Linux 5 theme, with the ladybirds, is derived from an old RedHat
wallpaper (either from RedHat 7 or 9).  So the image must have been
released under some sort of open license to be included on RedHat, but I
don't know what the license was or who is the copyright holder.

The Grasshopper image is (or was) on several public free-wallpaper
websites and clearly credited to Marcin Jankowski but I was not able to
find further license info or to contact Marcin, so I've used it without
permission.

Cheers,

TIM

On Wed, 2013-09-04 at 15:17 +0100, Sasa Paporovic wrote:
>   
> 
> Hi there,
> 
> I want to use some themes/logos/icons  of different Linux
> distributions in a paper. One of the affected one is Bio-Linux. I have
> downloaded the theme package from
> 
> 
> http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/all/
> 
> 
> After an examination with file-roller I was not able to find any
> license information either for the package nor for a single file. EXIF
> data shows also no license information.
> 
> 
> So, just this little mail. I want to ask if it is possible to get some
> license information or the simple permission to use the two .jpg in
> 
> 
> /usr/share/backgrounds/
> 
> 
> of the package.
> 
> 
> The first is the biolinux 5 theme, the second is a designed one by
> Marcin Jankowski.
> 
> 
> Could you forward if needed?
> 
> 
> Thanks
> 
> 
> Sasa Paporovic
> 
> 

-- 
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  Wed Sep  4 12:07:00 2013
From: sasa.paporovic at fh-bielefeld.de (Sasa Paporovic)
Date: Wed, 04 Sep 2013 18:07:00 +0200
Subject: [Bio-Linux] license of Bio-Linux artwork in package themes-v7
In-Reply-To: <75a0a196d8176.52275a9d@fh-bielefeld.de>
References: <74c0d7cadc222.52273ac3@fh-bielefeld.de>
	<76f0aad0dc7b0.52273b01@fh-bielefeld.de>
	<74a09f6edd619.52273b3e@fh-bielefeld.de>
	<7480cf6adbae4.52273dd3@fh-bielefeld.de>
	<71b09b29da33c.52273e0f@fh-bielefeld.de>
	<7780f9a1dc332.522740a5@fh-bielefeld.de>
	<7620f297ded30.52275cff@fh-bielefeld.de>
	<1378309534.25700.254.camel@balisaur>
	<762082cbdd1d1.5227592e@fh-bielefeld.de>
	<71b0e40bdd7d8.522759a8@fh-bielefeld.de>
	<7620b07ad9c64.52275a22@fh-bielefeld.de>
	<75a0a196d8176.52275a9d@fh-bielefeld.de>
Message-ID: <74b09befd99c3.522776c4@fh-bielefeld.de>

Thanks Tim,

mhhh, I tend to the grashopper:) 

greetings

Sasa

Am 04.09.13 schrieb Tim Booth  <tbooth at ceh.ac.uk>:
> Hi Sasa,
> 
> Unfortunately I don't have specific license information for these files
> but here's what I know:
> 
> The Bio-Linux 5 theme, with the ladybirds, is derived from an old RedHat
> wallpaper (either from RedHat 7 or 9). So the image must have been
> released under some sort of open license to be included on RedHat, but I
> don't know what the license was or who is the copyright holder.
> 
> The Grasshopper image is (or was) on several public free-wallpaper
> websites and clearly credited to Marcin Jankowski but I was not able to
> find further license info or to contact Marcin, so I've used it without
> permission.
> 
> Cheers,
> 
> TIM
> 
> On Wed, 2013-09-04 at 15:17 +0100, Sasa Paporovic wrote:
> > 
> > 
> > Hi there,
> > 
> > I want to use some themes/logos/icons of different Linux
> > distributions in a paper. One of the affected one is Bio-Linux. I have
> > downloaded the theme package from
> > 
> > 
> > http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/all/
> > 
> > 
> > After an examination with file-roller I was not able to find any
> > license information either for the package nor for a single file. EXIF
> > data shows also no license information.
> > 
> > 
> > So, just this little mail. I want to ask if it is possible to get some
> > license information or the simple permission to use the two .jpg in
> > 
> > 
> > /usr/share/backgrounds/
> > 
> > 
> > of the package.
> > 
> > 
> > The first is the biolinux 5 theme, the second is a designed one by
> > Marcin Jankowski.
> > 
> > 
> > Could you forward if needed?
> > 
> > 
> > Thanks
> > 
> > 
> > Sasa Paporovic
> > 
> > 
> 
> -- 
> 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
> 
> 
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From tony.travis at abdn.ac.uk  Thu Sep  5 05:32:07 2013
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 05 Sep 2013 10:32:07 +0100
Subject: [Bio-Linux] license of Bio-Linux artwork in package themes-v7
In-Reply-To: <74b09befd99c3.522776c4@fh-bielefeld.de>
References: <74c0d7cadc222.52273ac3@fh-bielefeld.de>
	<76f0aad0dc7b0.52273b01@fh-bielefeld.de>
	<74a09f6edd619.52273b3e@fh-bielefeld.de>
	<7480cf6adbae4.52273dd3@fh-bielefeld.de>
	<71b09b29da33c.52273e0f@fh-bielefeld.de>
	<7780f9a1dc332.522740a5@fh-bielefeld.de>
	<7620f297ded30.52275cff@fh-bielefeld.de>
	<1378309534.25700.254.camel@balisaur>
	<762082cbdd1d1.5227592e@fh-bielefeld.de>
	<71b0e40bdd7d8.522759a8@fh-bielefeld.de>
	<7620b07ad9c64.52275a22@fh-bielefeld.de>
	<75a0a196d8176.52275a9d@fh-bielefeld.de>
	<74b09befd99c3.522776c4@fh-bielefeld.de>
Message-ID: <52284F97.4070907@abdn.ac.uk>

On 04/09/13 17:07, Sasa Paporovic wrote:
> Thanks Tim,
> 
> mhhh, I tend to the grashopper:)

Hi, Sasa.

Me too ;-)

"If that is our destiny, you cannot change it. But do not go with fear,
Grasshopper; fear is eternal darkness. Go instead with inner strength,
for it is like a deep river into which all streams flow. It increases,
always moving forward; and soon, there is nothing that can stand in it's
way." -- Master Po

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



From Csaba.Miskey at pei.de  Fri Sep  6 08:24:37 2013
From: Csaba.Miskey at pei.de (Miskey, Csaba)
Date: Fri, 6 Sep 2013 12:24:37 +0000
Subject: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
Message-ID: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>

Dear Guys,

I wonder if Jeremy's problem with Tophat (error when trying to run it) was solved by updating to 2.0.9.
My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot make it run. (Bowtie accepts and runs ok with the same fastqsanger file with which Tophat throws the error. Though, as I figured the two mappers take the same set of indexes).

Any help would be greatly appreciated!

Best wishes,

Csaba
(new in the field)


Hi Jeremy,

I've pushed the update through for Tophat so it should become available
later today.

Note that bowtie is a legacy program that is unlikely to be updated
again.  The latest bowtie2 is packaged separately in the bowtie2 package
(currently 2.1.0).

Cheers,

TIM

On Tue, 2013-08-27 at 06:44 +0100, Jeremy Shearman wrote:
> Hi Tim
>              Can you please update the bio-linux tophat version to
> v2.0.9 because the current bio-linux version (2.0.8) is not compatible
> with the current bio-linux version of bowtie (v1.0.0) and throws an
> error when you try and run tophat.
>
> Thanks
> Jeremy

Csaba Miskey Ph.D.

Paul Ehrlich Institut
Medical Biotechnology
Paul Ehrich Str. 51-59
63225 Langen, Germany

Tel: +49 06103 773407
csaba.miskey at pei.de

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From jeremy.she at biotec.or.th  Fri Sep  6 09:52:47 2013
From: jeremy.she at biotec.or.th (Jeremy Shearman)
Date: Fri, 6 Sep 2013 13:52:47 +0000
Subject: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
In-Reply-To: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
References: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
Message-ID: <u4ooaxavnt31tr42ylljkirb.1378475562268@email.android.com>

Hi
     Yes upgrading fixed my problem.  Try running from the terminal using the fastq file, if that works it has to be a galaxy issue.


Sent from Samsung Mobile



-------- Original message --------
From: "Miskey, Csaba" <Csaba.Miskey at pei.de>
Date: 06/09/2013 19:25 (GMT+07:00)
To: bio-linux at nebclists.nerc.ac.uk
Cc: tbooth at ceh.ac.uk,Jeremy Shearman <jeremy.she at biotec.or.th>
Subject: Biolinux7_Galaxy_Tophat_error


Dear Guys,

I wonder if Jeremy?s problem with Tophat (error when trying to run it) was solved by updating to 2.0.9.
My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot make it run. (Bowtie accepts and runs ok with the same fastqsanger file with which Tophat throws the error. Though, as I figured the two mappers take the same set of indexes).

Any help would be greatly appreciated!

Best wishes,

Csaba
(new in the field)


Hi Jeremy,

I've pushed the update through for Tophat so it should become available
later today.

Note that bowtie is a legacy program that is unlikely to be updated
again.  The latest bowtie2 is packaged separately in the bowtie2 package
(currently 2.1.0).

Cheers,

TIM

On Tue, 2013-08-27 at 06:44 +0100, Jeremy Shearman wrote:
> Hi Tim
>              Can you please update the bio-linux tophat version to
> v2.0.9 because the current bio-linux version (2.0.8) is not compatible
> with the current bio-linux version of bowtie (v1.0.0) and throws an
> error when you try and run tophat.
>
> Thanks
> Jeremy

Csaba Miskey Ph.D.

Paul Ehrlich Institut
Medical Biotechnology
Paul Ehrich Str. 51-59
63225 Langen, Germany

Tel: +49 06103 773407
csaba.miskey at pei.de

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From tbooth at ceh.ac.uk  Fri Sep  6 10:34:33 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 6 Sep 2013 15:34:33 +0100
Subject: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
In-Reply-To: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
References: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
Message-ID: <1378478073.25700.325.camel@balisaur>

Hi Csaba,

Welcome to the Bio-Linux list.  You say that Tophat is giving you an
error but you've not told us what the error message actually says, so
it's hard to guess what the problem might be.

I've tested Tophat on the standard test data that they provide, both
running via Galaxy and on the command line, and both seem to work, but
I've not done any more extensive testing or used the software in anger.
My impression is that Tophat in Galaxy always uses Bowtie2 (they don't
expose the option to select Bowtie1) so I don't think this can be
related to Jeremy's problem.  If you open a terminal and type:

bowtie2 --version

What do you get?

Cheers,

TIM

On Fri, 2013-09-06 at 13:24 +0100, Miskey, Csaba wrote:
> Dear Guys,
> 
>  
> 
> I wonder if Jeremy?s problem with Tophat (error when trying to run it)
> was solved by updating to 2.0.9.
> 
> My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot
> make it run. (Bowtie accepts and runs ok with the same fastqsanger
> file with which Tophat throws the error. Though, as I figured the two
> mappers take the same set of indexes).
> 
>  
> 
> Any help would be greatly appreciated!
> 
>  



From Csaba.Miskey at pei.de  Fri Sep  6 11:48:39 2013
From: Csaba.Miskey at pei.de (Miskey, Csaba)
Date: Fri, 6 Sep 2013 15:48:39 +0000
Subject: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
In-Reply-To: <1378478073.25700.325.camel@balisaur>
References: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
	<1378478073.25700.325.camel@balisaur>
Message-ID: <29C374DAE8DE4042A02F2504E4CC08C8564C2D1D@sv-exch-02.ad.pei.de>

Hi Tim,

Thanks for your reply!

The error msg. I got in Galaxy:
0 bytes
An error occurred running this job: TopHat v2.0.9
TopHat v2.0.9
tophat -p 4 /var/lib/galaxy-server/genomes/hg19/bowtie/base/hg19 /usr/lib/galaxy-server/database/files/000/dataset_80.dat
Error in tophat:

[2013-09-05 19:54:18] Beginning TopHat run (v2.0.9)

But then I might see the problem.
In Galaxy there are two tools to choose from <Tophat for Illumina> and <Tophat2>. Both of them however call TopHat2!
And Tophat2 uses different indexes from Tophat (old). As they say in the galaxy wiki:
< Bowtie and Tophat use the same index set, and Bowtie2 and Tophat2 use the same index set, but Bowtie/Tophat and Bowtie2/Tophat2 do not use the same index set.>
So I thought that by clicking the <Tophat for Illumina> tool I'd fine with my Bowtie indexes. I do not have indexes for Bowtie2!
So my Bowtie works fine but since <Tophat for Illumina> calls Tophat2 it does not find indexes for running.
Right?

Would    sudo  bowtie-build -f hg19.fa hg19   solve the problem? (found in: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup)
(I do not have admin rights, and grasping  Linux is yet to accomplish too, hah! )

My Bowtie2 version:

bowtie2 --version               
/usr/bin/bowtie2-align version 2.1.0
64-bit
Built on wani09
Tue Apr 30 09:03:44 UTC 2013
Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 
Options: -O3 -m64 -msse2 -funroll-loops -g3 
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Many thanks again!

Cheers,

Csaba

-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: Freitag, 6. September 2013 16:35
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Biolinux7_Galaxy_Tophat_error

Hi Csaba,

Welcome to the Bio-Linux list.  You say that Tophat is giving you an error but you've not told us what the error message actually says, so it's hard to guess what the problem might be.

I've tested Tophat on the standard test data that they provide, both running via Galaxy and on the command line, and both seem to work, but I've not done any more extensive testing or used the software in anger.
My impression is that Tophat in Galaxy always uses Bowtie2 (they don't expose the option to select Bowtie1) so I don't think this can be related to Jeremy's problem.  If you open a terminal and type:

bowtie2 --version

What do you get?

Cheers,

TIM

On Fri, 2013-09-06 at 13:24 +0100, Miskey, Csaba wrote:
> Dear Guys,
> 
>  
> 
> I wonder if Jeremy?s problem with Tophat (error when trying to run it) 
> was solved by updating to 2.0.9.
> 
> My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot 
> make it run. (Bowtie accepts and runs ok with the same fastqsanger 
> file with which Tophat throws the error. Though, as I figured the two 
> mappers take the same set of indexes).
> 
>  
> 
> Any help would be greatly appreciated!
> 
>  

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

From tbooth at ceh.ac.uk  Fri Sep  6 12:34:13 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 6 Sep 2013 17:34:13 +0100
Subject: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
In-Reply-To: <29C374DAE8DE4042A02F2504E4CC08C8564C2D1D@sv-exch-02.ad.pei.de>
References: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
	<1378478073.25700.325.camel@balisaur>
	<29C374DAE8DE4042A02F2504E4CC08C8564C2D1D@sv-exch-02.ad.pei.de>
Message-ID: <1378485253.25700.339.camel@balisaur>

Hi,

OK, thanks for the info.  I must say, I find Galaxy quite confusing when
working out which data needs to be fed to which programs.  I always tend
to use the command line as it's faster and there is one less layer of
complexity.

Bio-Linux comes with Tophat which is actually Tophat2 (2.0.9 as you saw
below) and it doesn't matter if you run tophat or tophat2 as they are
both the same program.  But bowtie and bowtie2 are separate programs,
installed as separate packages.  You can find out what programs these
packages provide like so:

tbooth at balisaur[tbooth]dpkg -L bowtie | grep /usr/bin.
/usr/bin/bowtie-build-debug
/usr/bin/bowtie-build
/usr/bin/bowtie-inspect
/usr/bin/bowtie
/usr/bin/bowtie-debug
/usr/bin/bowtie-inspect-debug

tbooth at balisaur[tbooth]dpkg -L bowtie2 | grep /usr/bin.
/usr/bin/bowtie2-align
/usr/bin/bowtie2-inspect
/usr/bin/bowtie2
/usr/bin/bowtie2-build
/usr/bin/bowtie2-inspect-debug
/usr/bin/bowtie2-build-debug
/usr/bin/bowtie2-align-debug

I'm not sure what's up with the index files, but I'm hoping that
re-indexing your genome with bowtie2-build (not bowtie-build) will solve
the problem.  Any joy with that?

Cheers,

TIM

On Fri, 2013-09-06 at 16:48 +0100, Miskey, Csaba wrote:
> Hi Tim,
> 
> Thanks for your reply!
> 
> The error msg. I got in Galaxy:
> 0 bytes
> An error occurred running this job: TopHat v2.0.9
> TopHat v2.0.9
> tophat -p 4 /var/lib/galaxy-server/genomes/hg19/bowtie/base/hg19 /usr/lib/galaxy-server/database/files/000/dataset_80.dat
> Error in tophat:
> 
> [2013-09-05 19:54:18] Beginning TopHat run (v2.0.9)
> 
> But then I might see the problem.
> In Galaxy there are two tools to choose from <Tophat for Illumina> and <Tophat2>. Both of them however call TopHat2!
> And Tophat2 uses different indexes from Tophat (old). As they say in the galaxy wiki:
> < Bowtie and Tophat use the same index set, and Bowtie2 and Tophat2 use the same index set, but Bowtie/Tophat and Bowtie2/Tophat2 do not use the same index set.>
> So I thought that by clicking the <Tophat for Illumina> tool I'd fine with my Bowtie indexes. I do not have indexes for Bowtie2!
> So my Bowtie works fine but since <Tophat for Illumina> calls Tophat2 it does not find indexes for running.
> Right?
> 
> Would    sudo  bowtie-build -f hg19.fa hg19   solve the problem? (found in: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup)
> (I do not have admin rights, and grasping  Linux is yet to accomplish too, hah! )
> 
> My Bowtie2 version:
> 
> bowtie2 --version               
> /usr/bin/bowtie2-align version 2.1.0
> 64-bit
> Built on wani09
> Tue Apr 30 09:03:44 UTC 2013
> Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 
> Options: -O3 -m64 -msse2 -funroll-loops -g3 
> Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
> 
> Many thanks again!
> 
> Cheers,
> 
> Csaba
> 
> -----Original Message-----
> From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
> Sent: Freitag, 6. September 2013 16:35
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
> 
> Hi Csaba,
> 
> Welcome to the Bio-Linux list.  You say that Tophat is giving you an error but you've not told us what the error message actually says, so it's hard to guess what the problem might be.
> 
> I've tested Tophat on the standard test data that they provide, both running via Galaxy and on the command line, and both seem to work, but I've not done any more extensive testing or used the software in anger.
> My impression is that Tophat in Galaxy always uses Bowtie2 (they don't expose the option to select Bowtie1) so I don't think this can be related to Jeremy's problem.  If you open a terminal and type:
> 
> bowtie2 --version
> 
> What do you get?
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2013-09-06 at 13:24 +0100, Miskey, Csaba wrote:
> > Dear Guys,
> > 
> >  
> > 
> > I wonder if Jeremy?s problem with Tophat (error when trying to run it) 
> > was solved by updating to 2.0.9.
> > 
> > My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot 
> > make it run. (Bowtie accepts and runs ok with the same fastqsanger 
> > file with which Tophat throws the error. Though, as I figured the two 
> > mappers take the same set of indexes).
> > 
> >  
> > 
> > Any help would be greatly appreciated!
> > 
> >  
> 
> _______________________________________________
> 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 Csaba.Miskey at pei.de  Fri Sep  6 13:58:12 2013
From: Csaba.Miskey at pei.de (Miskey, Csaba)
Date: Fri, 6 Sep 2013 17:58:12 +0000
Subject: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
In-Reply-To: <1378485253.25700.339.camel@balisaur>
References: <29C374DAE8DE4042A02F2504E4CC08C8564C2CC6@sv-exch-02.ad.pei.de>
	<1378478073.25700.325.camel@balisaur>
	<29C374DAE8DE4042A02F2504E4CC08C8564C2D1D@sv-exch-02.ad.pei.de>
	<1378485253.25700.339.camel@balisaur>
Message-ID: <29C374DAE8DE4042A02F2504E4CC08C8564C2D4D@sv-exch-02.ad.pei.de>

Hi Tim,

Ok, then we agree that I need the bowtie2 indexes.
Many thanks for your help again to figure it out!

Cheers,

Csaba


-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: Freitag, 6. September 2013 18:34
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Biolinux7_Galaxy_Tophat_error

Hi,

OK, thanks for the info.  I must say, I find Galaxy quite confusing when working out which data needs to be fed to which programs.  I always tend to use the command line as it's faster and there is one less layer of complexity.

Bio-Linux comes with Tophat which is actually Tophat2 (2.0.9 as you saw
below) and it doesn't matter if you run tophat or tophat2 as they are both the same program.  But bowtie and bowtie2 are separate programs, installed as separate packages.  You can find out what programs these packages provide like so:

tbooth at balisaur[tbooth]dpkg -L bowtie | grep /usr/bin.
/usr/bin/bowtie-build-debug
/usr/bin/bowtie-build
/usr/bin/bowtie-inspect
/usr/bin/bowtie
/usr/bin/bowtie-debug
/usr/bin/bowtie-inspect-debug

tbooth at balisaur[tbooth]dpkg -L bowtie2 | grep /usr/bin.
/usr/bin/bowtie2-align
/usr/bin/bowtie2-inspect
/usr/bin/bowtie2
/usr/bin/bowtie2-build
/usr/bin/bowtie2-inspect-debug
/usr/bin/bowtie2-build-debug
/usr/bin/bowtie2-align-debug

I'm not sure what's up with the index files, but I'm hoping that re-indexing your genome with bowtie2-build (not bowtie-build) will solve the problem.  Any joy with that?

Cheers,

TIM

On Fri, 2013-09-06 at 16:48 +0100, Miskey, Csaba wrote:
> Hi Tim,
> 
> Thanks for your reply!
> 
> The error msg. I got in Galaxy:
> 0 bytes
> An error occurred running this job: TopHat v2.0.9 TopHat v2.0.9 tophat 
> -p 4 /var/lib/galaxy-server/genomes/hg19/bowtie/base/hg19 
> /usr/lib/galaxy-server/database/files/000/dataset_80.dat
> Error in tophat:
> 
> [2013-09-05 19:54:18] Beginning TopHat run (v2.0.9)
> 
> But then I might see the problem.
> In Galaxy there are two tools to choose from <Tophat for Illumina> and <Tophat2>. Both of them however call TopHat2!
> And Tophat2 uses different indexes from Tophat (old). As they say in the galaxy wiki:
> < Bowtie and Tophat use the same index set, and Bowtie2 and Tophat2 
> use the same index set, but Bowtie/Tophat and Bowtie2/Tophat2 do not use the same index set.> So I thought that by clicking the <Tophat for Illumina> tool I'd fine with my Bowtie indexes. I do not have indexes for Bowtie2!
> So my Bowtie works fine but since <Tophat for Illumina> calls Tophat2 it does not find indexes for running.
> Right?
> 
> Would    sudo  bowtie-build -f hg19.fa hg19   solve the problem? (found in: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup)
> (I do not have admin rights, and grasping  Linux is yet to accomplish 
> too, hah! )
> 
> My Bowtie2 version:
> 
> bowtie2 --version               
> /usr/bin/bowtie2-align version 2.1.0
> 64-bit
> Built on wani09
> Tue Apr 30 09:03:44 UTC 2013
> Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
> Options: -O3 -m64 -msse2 -funroll-loops -g3 Sizeof {int, long, long 
> long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
> 
> Many thanks again!
> 
> Cheers,
> 
> Csaba
> 
> -----Original Message-----
> From: bio-linux-bounces at nebclists.nerc.ac.uk 
> [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
> Sent: Freitag, 6. September 2013 16:35
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
> 
> Hi Csaba,
> 
> Welcome to the Bio-Linux list.  You say that Tophat is giving you an error but you've not told us what the error message actually says, so it's hard to guess what the problem might be.
> 
> I've tested Tophat on the standard test data that they provide, both running via Galaxy and on the command line, and both seem to work, but I've not done any more extensive testing or used the software in anger.
> My impression is that Tophat in Galaxy always uses Bowtie2 (they don't expose the option to select Bowtie1) so I don't think this can be related to Jeremy's problem.  If you open a terminal and type:
> 
> bowtie2 --version
> 
> What do you get?
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2013-09-06 at 13:24 +0100, Miskey, Csaba wrote:
> > Dear Guys,
> > 
> >  
> > 
> > I wonder if Jeremy?s problem with Tophat (error when trying to run 
> > it) was solved by updating to 2.0.9.
> > 
> > My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still 
> > cannot make it run. (Bowtie accepts and runs ok with the same 
> > fastqsanger file with which Tophat throws the error. Though, as I 
> > figured the two mappers take the same set of indexes).
> > 
> >  
> > 
> > Any help would be greatly appreciated!
> > 
> >  
> 
> _______________________________________________
> 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 guillermo.lopez at unimelb.edu.au  Sun Sep  8 20:07:15 2013
From: guillermo.lopez at unimelb.edu.au (Guillermo Hugo Lopez Campos)
Date: Mon, 9 Sep 2013 00:07:15 +0000
Subject: [Bio-Linux] Problems updating biolinux
Message-ID: <CE534E52.3751%glopez@unimelb.edu.au>

Hello,

I haven't used my biolinux for a while (around 1 month) and now when I I cannot update it because it says that the update requires the installation of untrusted packages and it doesn't allow me to continue with it. Any ideas about why could this be happening and how to solve it?

Thanks in advance

Guillermo
---------------------------------------------------------------------------------
Guillermo Lopez Campos
HaBIC - Health and Biomedical Informatics Centre
Melbourne Medical School
The University of Melbourne
Level 1, 202 Berkeley Street. 3010 VIC
Telephone: +61 3 9035 7544
---------------------------------------------------------------------------------
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From kissaj at miamioh.edu  Sun Sep  8 21:06:38 2013
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Sun, 8 Sep 2013 21:06:38 -0400
Subject: [Bio-Linux] Problems updating biolinux
In-Reply-To: <CE534E52.3751%glopez@unimelb.edu.au>
References: <CE534E52.3751%glopez@unimelb.edu.au>
Message-ID: <E3E177E2-EF5F-4301-954F-6891B4AB7A79@miamioh.edu>

Hello, 

  It's a package signing issue.  If you trust the packages, then you can update & upgrade via the CLI.

$ sudo apt-get update

$ sudo apt-get upgrade

The last command will complain about the unsigned packages, but it will permit you to override that warning and upgrade anyway - whereas the GUI (update-mangaler) will not.

Regards,
____________________________
Andor J Kiss
eMAIL: kissaj at MiamiOH.edu

On Sep 8, 2013, at 8:07 PM, Guillermo Hugo Lopez Campos <guillermo.lopez at unimelb.edu.au> wrote:

> Hello, 
> 
> I haven't used my biolinux for a while (around 1 month) and now when I I cannot update it because it says that the update requires the installation of untrusted packages and it doesn't allow me to continue with it. Any ideas about why could this be happening and how to solve it? 
> 
> Thanks in advance
> 
> Guillermo
> ---------------------------------------------------------------------------------
> Guillermo Lopez Campos
> HaBIC - Health and Biomedical Informatics Centre
> Melbourne Medical School
> The University of Melbourne
> Level 1, 202 Berkeley Street. 3010 VIC
> Telephone: +61 3 9035 7544
> ---------------------------------------------------------------------------------
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
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From tbooth at ceh.ac.uk  Thu Sep 12 06:31:01 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 12 Sep 2013 11:31:01 +0100
Subject: [Bio-Linux] Problems updating biolinux
In-Reply-To: <E3E177E2-EF5F-4301-954F-6891B4AB7A79@miamioh.edu>
References: <CE534E52.3751%glopez@unimelb.edu.au>
	<E3E177E2-EF5F-4301-954F-6891B4AB7A79@miamioh.edu>
Message-ID: <1378981861.3187.24.camel@balisaur>

Hi Guillermo,

Andor is right that you can just ignore the authentication issue and
force the package installations, but this doesn't really address the
problem.  Sometimes the signatures get temporarily out of sync with the
server but in general secure APT should work seamlessly.

If you run "sudo apt-get update" on the command line just now and still
get signing errors then let me know - specifically the bit where it says
"NO_PUBKEY ..." and which key it is complaining about, and I'll see what
might need fixing.

On a related note, you may well find that the graphical updater is
unable to upgrade the package "bio-linux-glimmer3".  This is my fault
for not quite understanding how to do package renaming neatly.  The
solution is:

sudo apt-get install glimmer3 bio-linux-glimmer3

and say yes to removing tigr-glimmer, which is the old name for the
package.  Note that Glimmer3 hasn't actually been updated, it's just
that the old name makes no sense any more.

Cheers,

TIM

On Mon, 2013-09-09 at 02:06 +0100, Andor J Kiss wrote:
> Hello, 
> 
> 
>   It's a package signing issue.  If you trust the packages, then you
> can update & upgrade via the CLI.
> 
> 
> $ sudo apt-get update
> 
> 
> $ sudo apt-get upgrade
> 
> 
> The last command will complain about the unsigned packages, but it
> will permit you to override that warning and upgrade anyway - whereas
> the GUI (update-mangaler) will not.
> 
> 
> Regards,
> ____________________________
> Andor J Kiss
> eMAIL: kissaj at MiamiOH.edu
> 
> On Sep 8, 2013, at 8:07 PM, Guillermo Hugo Lopez Campos
> <guillermo.lopez at unimelb.edu.au> wrote:
> 
> 
> > Hello, 
> > 
> > 
> > I haven't used my biolinux for a while (around 1 month) and now when
> > I I cannot update it because it says that the update requires the
> > installation of untrusted packages and it doesn't allow me to
> > continue with it. Any ideas about why could this be happening and
> > how to solve it? 
> > 
> > 
> > Thanks in advance
> > 
> > 
> > Guillermo
> > ---------------------------------------------------------------------------------
> > Guillermo Lopez Campos
> > HaBIC - Health and Biomedical Informatics Centre
> > Melbourne Medical School
> > The University of Melbourne
> > 
> > 
> > Level 1, 202 Berkeley Street. 3010 VIC
> > Telephone: +61 3 9035 7544
> > ---------------------------------------------------------------------------------
> > _______________________________________________
> > 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 Christopher.Dubay at providence.org  Mon Sep 16 13:08:29 2013
From: Christopher.Dubay at providence.org (Dubay, Christopher)
Date: Mon, 16 Sep 2013 17:08:29 +0000
Subject: [Bio-Linux] BioLinux/Ubuntu Package Manager Question
Message-ID: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>

> To whom it may concern:

>

> I had a question for you on the BioLinux/Ubuntu package manager.

>

> A few of our BioLinux VMs are behind a firewall that is not allowing the package manager to find updates to the system.

>

> What do you think would be the easiest way for us to get these VMs updated? We do have some machines that can access the Ubuntu and NEBC/NECR BioLinux repositories, so we could download the updates, but I don't know enough Linux to know the best way to do this. Our IT staff gets nervous with using proxies, so a file transfer based method would be best.

>

> Thanks in advance for your time responding to this query...

>

> Christopher

>

> Christopher Dubay, PhD

> Biomedical Informatics Team

> Immune Monitoring Laboratory

> Laboratory of Molecular and Tumor Immunology Earle A. Chiles Research

> Institute Providence Cancer Center

> 4805 NE Glisan St.- 2N57

> Portland, OR 97213  USA

> T: (503) 215-7981

> F: (503) 215-6841

>

> christopher.dubay at providence.org<mailto:christopher.dubay at providence.org>

>


________________________________

This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.
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From tbooth at ceh.ac.uk  Mon Sep 16 14:03:42 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 16 Sep 2013 19:03:42 +0100
Subject: [Bio-Linux] BioLinux/Ubuntu Package Manager Question
In-Reply-To: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>
References: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>
Message-ID: <1379354622.3187.417.camel@balisaur>

Hi Christopher,

The short answer is you need a web proxy server, whatever the IT staff
say.

Without this, you could try to manually copy the updates as .deb files
from /var/cache/apt/archives on an on-line machine and install them on
the VMs with "sudo dpkg -i *.deb" but this is never going to be
practical if you want regular updates.  And it assumes that the updates
for the VMs and the on-line machine are identical, which they probably
aren't because you'll add and remove packages on different machines.

So really you need some sort of web proxy that permits the VMs to
retrieve package updates themselves.  The proxy only needs to permit
connections to the servers listed in sources.list, which you can list
like so (it varies depending on locale so I can't just paste the list):

cat /etc/apt/sources.list /etc/apt/sources.list.d/* | grep -o 'http[^ ]*' | sort -u

Can your IT people be persuaded that a web proxy only accessing a small
list of known servers is safe?  It does seem rather crazy to connect
your institute to the high-speed internet access you undoubtedly have
and then to spend your time shuttling files back and forth manually.

Hope that helps.

Cheers,

TIM

On Mon, 2013-09-16 at 18:08 +0100, Dubay, Christopher wrote:
> > To whom it may concern:
> 
> > 
> 
> > I had a question for you on the BioLinux/Ubuntu package manager.
> 
> > 
> 
> > A few of our BioLinux VMs are behind a firewall that is not allowing
> the package manager to find updates to the system.
> 
> > 
> 
> > What do you think would be the easiest way for us to get these VMs
> updated? We do have some machines that can access the Ubuntu and
> NEBC/NECR BioLinux repositories, so we could download the updates, but
> I don?t know enough Linux to know the best way to do this. Our IT
> staff gets nervous with using proxies, so a file transfer based method
> would be best.
> 
> > 
> 
> > Thanks in advance for your time responding to this query...
> 
> > 
> 
> > Christopher
> 
> > 
> 
> > Christopher Dubay, PhD
> 
> > Biomedical Informatics Team
> 
> > Immune Monitoring Laboratory
> 
> > Laboratory of Molecular and Tumor Immunology Earle A. Chiles
> Research
> 
> > Institute Providence Cancer Center
> 
> > 4805 NE Glisan St.- 2N57
> 
> > Portland, OR 97213  USA
> 
> > T: (503) 215-7981
> 
> > F: (503) 215-6841
> 
> > 
> 
> > christopher.dubay at providence.org
> 
> > 
> 
>  
> 
> 
> 
> 
> ______________________________________________________________________
> 
> This message is intended for the sole use of the addressee, and may
> contain information that is privileged, confidential and exempt from
> disclosure under applicable law. If you are not the addressee you are
> hereby notified that you may not use, copy, disclose, or distribute to
> anyone the message or any information contained in the message. If you
> have received this message in error, please immediately advise the
> sender by reply email and delete this message.

-- 
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 jeremy.she at biotec.or.th  Tue Sep 17 05:19:14 2013
From: jeremy.she at biotec.or.th (Jeremy Shearman)
Date: Tue, 17 Sep 2013 09:19:14 +0000
Subject: [Bio-Linux] msatfinder pipeline fails to find primers
Message-ID: <5E8AFED5C97C894D8554A1D98682F90C3C7EB7@SPIMBN1B.biotec.or.th>

I recently tried msatfinder in bio-linux7 to compare it to misa that a colleague used. Msatfinder seemed to find all the same microsatellite sequences but on my system completely failed to produce primers with the message "No valid primers found for ..." printed to the terminal. I know there are valid primers because misa found them (but I don't know what versions of things) and when I took the fasta sequence from the msatfinder FASTA output folder, web based primer3 found several primer pairs.

To troubleshoot I took a random sequence from human chr1
(http://www.ncbi.nlm.nih.gov/nuccore/NC_000001.10?report=fasta&from=3556583&to=3665309) and ran msatfinder on it.

Here is the final microsat results from the terminal dump:
Found (taaa)5 msat at 104492:
FT   repeat_region   104492..104511
FT                   /label={taaa}5
FT                   /note="(taaa)5"
FT                   /note="Coding:  0"
FT                   /note="Gene:      N/A"
FT                   /note="Product: N/A"
FT                   /note="Protein: N/A"
Opening output file 224589800_3556583-3665309.msat_tab
Writing MINE file 224589800_3556583-3665309.104492.taaa.5.db
Opening fasta FILE Fasta/224589800_3556583-3665309.104492.taaa.5.fasta
Determining PCR primers.
Outfile: Primers/224589800_3556583-3665309.104492.taaa.5.primers.txt
Running command: /usr/bin/eprimer3 -sequence Primers/224589800_3556583-3665309.104492.taaa.5.temp -outfile Primers/224589800_3556583-3665309.104492.taaa.5.primers.txt -target 298,320 -primer
Unlinking file: Primers/224589800_3556583-3665309.104492.taaa.5.temp
No valid primers found for 224589800_3556583-3665309
-----


A total of 1 files surveyed
Hs_chr_1_3556583-3665309
Msatfinder finished!

When I then went to the FASTA file (224589800_3556583-3665309.104492.taaa.5.fasta) primer3 on the web gave primers.

I turned on debugging info in the msatfinder.rc file which caused the temp file in the primers folder to not get deleted, running eprimer3 with that file gives this error:

Error: Missing SEQUENCE tag

Anyone know what the problem is?

Cheers
Jeremy

Jeremy Shearman, PhD
???????? ?????????
National Centre for Genetic Engineering and Biotechnology, NSTDA
113 Thailand Science Park, Phahonyothin Road, Klong1, Klong Luang, Pathumthani 12120
Ph: +66 2564 6700 ext. 3234       fax: +66 2564 6584

ReasearcherID: F-1618-2010
http://www.researcherid.com/rid/F-1618-2010
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From tony.travis at abdn.ac.uk  Tue Sep 17 05:26:00 2013
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 17 Sep 2013 10:26:00 +0100
Subject: [Bio-Linux] BioLinux/Ubuntu Package Manager Question
In-Reply-To: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>
References: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>
Message-ID: <52382028.5050001@abdn.ac.uk>

On 16/09/13 18:08, Dubay, Christopher wrote:
>> To whom it may concern:
>
>>
>
>> I had a question for you on the BioLinux/Ubuntu package manager.
>
>>
>
>> A few of our BioLinux VMs are behind a firewall that is not allowing
> the package manager to find updates to the system.
>
>>
>
>> What do you think would be the easiest way for us to get these VMs
> updated? We do have some machines that can access the Ubuntu and
> NEBC/NECR BioLinux repositories, so we could download the updates, but I
> don?t know enough Linux to know the best way to do this. Our IT staff
> gets nervous with using proxies, so a file transfer based method would
> be best.

Hi, Christopher.

The VM's should be using the host computer's NIC's to access the LAN.

Can you access the web from the host computer?

Check if an environment variable is set on the host:

  printenv http_proxy

If it is, use the same setting on your VM's:

  export http_proxy=http://myproxy.mydomain

Where myproxy.mydomain is the setting of http_proxy on the host OS.

To do this permanently, you need to configure APT to use a proxy. This
is how I do it for my workstation:

  vim /etc/apt/apt.conf.d/01proxy
  ...
  Acquire::http::Proxy "http://proxy.abdn.ac.uk:8080";
  ...

HTH,

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




The University of Aberdeen is a charity registered in Scotland, No SC013683.


From Christopher.Dubay at providence.org  Tue Sep 17 11:39:58 2013
From: Christopher.Dubay at providence.org (Dubay, Christopher)
Date: Tue, 17 Sep 2013 15:39:58 +0000
Subject: [Bio-Linux] BioLinux/Ubuntu Package Manager Question
In-Reply-To: <52382028.5050001@abdn.ac.uk>
References: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>,
	<52382028.5050001@abdn.ac.uk>
Message-ID: <3F9E65788480CD4282B12895264CC21413A47D85@WN35105.or.providence.org>

Tony,

Thanks for the quick reply.

Unfortunately, no I can not access the required Web sites from the host, due to corporate firewall restrictions. I can ask for firewall pinholes for work related web access needs, however I would rather avoid this for every machine running a BioLinux instance.

I do have one machine with the needed pinholes in the firewall, and so the question really is: how can I replicate or share the updates from this machine with others without setting up some kind of proxy ( e.g. With my own update repository, or other method)?

Hope that is more clear. Thanks...

Christopher
________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tony Travis [tony.travis at abdn.ac.uk]
Sent: Tuesday, September 17, 2013 2:26 AM
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] BioLinux/Ubuntu Package Manager Question

On 16/09/13 18:08, Dubay, Christopher wrote:
>> To whom it may concern:
>
>>
>
>> I had a question for you on the BioLinux/Ubuntu package manager.
>
>>
>
>> A few of our BioLinux VMs are behind a firewall that is not allowing
> the package manager to find updates to the system.
>
>>
>
>> What do you think would be the easiest way for us to get these VMs
> updated? We do have some machines that can access the Ubuntu and
> NEBC/NECR BioLinux repositories, so we could download the updates, but I
> don?t know enough Linux to know the best way to do this. Our IT staff
> gets nervous with using proxies, so a file transfer based method would
> be best.

Hi, Christopher.

The VM's should be using the host computer's NIC's to access the LAN.

Can you access the web from the host computer?

Check if an environment variable is set on the host:

  printenv http_proxy

If it is, use the same setting on your VM's:

  export http_proxy=http://myproxy.mydomain

Where myproxy.mydomain is the setting of http_proxy on the host OS.

To do this permanently, you need to configure APT to use a proxy. This
is how I do it for my workstation:

  vim /etc/apt/apt.conf.d/01proxy
  ...
  Acquire::http::Proxy "http://proxy.abdn.ac.uk:8080";
  ...

HTH,

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




The University of Aberdeen is a charity registered in Scotland, No SC013683.
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


________________________________

This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.



From A.J.Pemberton at bham.ac.uk  Tue Sep 17 11:50:42 2013
From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton)
Date: Tue, 17 Sep 2013 15:50:42 +0000
Subject: [Bio-Linux] BioLinux/Ubuntu Package Manager Question
In-Reply-To: <3F9E65788480CD4282B12895264CC21413A47D85@WN35105.or.providence.org>
References: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>,
	<52382028.5050001@abdn.ac.uk>
	<3F9E65788480CD4282B12895264CC21413A47D85@WN35105.or.providence.org>
Message-ID: <F457492129F2CE479A10341340E60260020A87@EX1.adf.bham.ac.uk>

Christopher,

Look into apt-mirror - there are a number of blogs and howtos on the web. Then you only need to update one system and update the rest from that,

Regards,

Tony P.


-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Dubay, Christopher
Sent: 17 September 2013 16:40
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] BioLinux/Ubuntu Package Manager Question

Tony,

Thanks for the quick reply.

Unfortunately, no I can not access the required Web sites from the host, due to corporate firewall restrictions. I can ask for firewall pinholes for work related web access needs, however I would rather avoid this for every machine running a BioLinux instance.

I do have one machine with the needed pinholes in the firewall, and so the question really is: how can I replicate or share the updates from this machine with others without setting up some kind of proxy ( e.g. With my own update repository, or other method)?

Hope that is more clear. Thanks...

Christopher
________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tony Travis [tony.travis at abdn.ac.uk]
Sent: Tuesday, September 17, 2013 2:26 AM
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] BioLinux/Ubuntu Package Manager Question

On 16/09/13 18:08, Dubay, Christopher wrote:
>> To whom it may concern:
>
>>
>
>> I had a question for you on the BioLinux/Ubuntu package manager.
>
>>
>
>> A few of our BioLinux VMs are behind a firewall that is not allowing
> the package manager to find updates to the system.
>
>>
>
>> What do you think would be the easiest way for us to get these VMs
> updated? We do have some machines that can access the Ubuntu and
> NEBC/NECR BioLinux repositories, so we could download the updates, but I
> don't know enough Linux to know the best way to do this. Our IT staff
> gets nervous with using proxies, so a file transfer based method would
> be best.

Hi, Christopher.

The VM's should be using the host computer's NIC's to access the LAN.

Can you access the web from the host computer?

Check if an environment variable is set on the host:

  printenv http_proxy

If it is, use the same setting on your VM's:

  export http_proxy=http://myproxy.mydomain

Where myproxy.mydomain is the setting of http_proxy on the host OS.

To do this permanently, you need to configure APT to use a proxy. This
is how I do it for my workstation:

  vim /etc/apt/apt.conf.d/01proxy
  ...
  Acquire::http::Proxy "http://proxy.abdn.ac.uk:8080";
  ...

HTH,

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




The University of Aberdeen is a charity registered in Scotland, No SC013683.
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


________________________________

This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


From Christopher.Dubay at providence.org  Wed Sep 18 13:28:28 2013
From: Christopher.Dubay at providence.org (Dubay, Christopher)
Date: Wed, 18 Sep 2013 17:28:28 +0000
Subject: [Bio-Linux] BioLinux/Ubuntu Package Manager Question
In-Reply-To: <F457492129F2CE479A10341340E60260020A87@EX1.adf.bham.ac.uk>
References: <3F9E65788480CD4282B12895264CC21413A47C24@WN35105.or.providence.org>,
	<52382028.5050001@abdn.ac.uk>
	<3F9E65788480CD4282B12895264CC21413A47D85@WN35105.or.providence.org>
	<F457492129F2CE479A10341340E60260020A87@EX1.adf.bham.ac.uk>
Message-ID: <3F9E65788480CD4282B12895264CC21413A47F78@WN35105.or.providence.org>

Thank you all for the ideas! I will try implementing them, and report back with what worked for me (sometime next week with any good luck!).

Christopher

-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Anthony Pemberton
Sent: Tuesday, September 17, 2013 8:51 AM
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] BioLinux/Ubuntu Package Manager Question

Christopher,

Look into apt-mirror - there are a number of blogs and howtos on the web. Then you only need to update one system and update the rest from that,

Regards,

Tony P.


-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Dubay, Christopher
Sent: 17 September 2013 16:40
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] BioLinux/Ubuntu Package Manager Question

Tony,

Thanks for the quick reply.

Unfortunately, no I can not access the required Web sites from the host, due to corporate firewall restrictions. I can ask for firewall pinholes for work related web access needs, however I would rather avoid this for every machine running a BioLinux instance.

I do have one machine with the needed pinholes in the firewall, and so the question really is: how can I replicate or share the updates from this machine with others without setting up some kind of proxy ( e.g. With my own update repository, or other method)?

Hope that is more clear. Thanks...

Christopher
________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tony Travis [tony.travis at abdn.ac.uk]
Sent: Tuesday, September 17, 2013 2:26 AM
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] BioLinux/Ubuntu Package Manager Question

On 16/09/13 18:08, Dubay, Christopher wrote:
>> To whom it may concern:
>
>>
>
>> I had a question for you on the BioLinux/Ubuntu package manager.
>
>>
>
>> A few of our BioLinux VMs are behind a firewall that is not allowing
> the package manager to find updates to the system.
>
>>
>
>> What do you think would be the easiest way for us to get these VMs
> updated? We do have some machines that can access the Ubuntu and
> NEBC/NECR BioLinux repositories, so we could download the updates, but
> I don't know enough Linux to know the best way to do this. Our IT
> staff gets nervous with using proxies, so a file transfer based method
> would be best.

Hi, Christopher.

The VM's should be using the host computer's NIC's to access the LAN.

Can you access the web from the host computer?

Check if an environment variable is set on the host:

  printenv http_proxy

If it is, use the same setting on your VM's:

  export http_proxy=http://myproxy.mydomain

Where myproxy.mydomain is the setting of http_proxy on the host OS.

To do this permanently, you need to configure APT to use a proxy. This is how I do it for my workstation:

  vim /etc/apt/apt.conf.d/01proxy
  ...
  Acquire::http::Proxy "http://proxy.abdn.ac.uk:8080";
  ...

HTH,

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




The University of Aberdeen is a charity registered in Scotland, No SC013683.
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


________________________________

This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.

_______________________________________________
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


________________________________

This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.