From kellert at ohsu.edu  Thu Aug 15 13:27:13 2013
From: kellert at ohsu.edu (Tom Keller)
Date: Thu, 15 Aug 2013 10:27:13 -0700
Subject: [Bio-Linux] RStudio with Bio-Linux
In-Reply-To: <mailman.1.1374577201.16181.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1374577201.16181.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <E1685117-7357-4EC0-9A79-FD9D15859717@ohsu.edu>

Hi Tim,
Is there a way to use RStudio with R from Bio-Linux?

thanks for your help.
Tom Keller
Thomas J. Keller, Ph.D.; Director, DNA Services Core Facility ; Oregon Health & Science University;
mailcode L220; 3181 SW Sam Jackson Park Rd; Portland, OR 97239; 503-494-2442

On Jul 23, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:

> Send Bio-Linux mailing list submissions to
> 	bio-linux at nebclists.nerc.ac.uk
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
> 	bio-linux-request at nebclists.nerc.ac.uk
> 
> You can reach the person managing the list at
> 	bio-linux-owner at nebclists.nerc.ac.uk
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
> 
> 
> Today's Topics:
> 
>   1. Bio-Linux updated image and new packages (Tim Booth)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 22 Jul 2013 16:55:06 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> Subject: [Bio-Linux] Bio-Linux updated image and new packages
> To: Bio-Linux mailing list <bio-linux at nebclists.nerc.ac.uk>
> Message-ID: <1374508506.10050.57.camel at balisaur>
> Content-Type: text/plain; charset="UTF-8"
> 
> Hi All,
> 
> I've put a new Bio-Linux image update on the website today (7.0.7).
> Existing users won't need to use this but I've added some new packages
> which you might be interested in installing on your machines (sudo
> apt-get install <packagename>):
> 
> abyss  (http://www.bcgsc.ca/platform/bioinfo/software/abyss)
> ray    (http://denovoassembler.sourceforge.net/)
> sickle (https://github.com/vsbuffalo/sickle)
> scythe (https://github.com/vsbuffalo/scythe)
> macs   (http://liulab.dfci.harvard.edu/MACS/)
> 
> The R environment has been upgraded to R3.0 and modules have been
> recompiled to work on the new R.  If you have installed extra modules
> and get an error about an incompatible R module you may need to run
> "install.packages(<modulename>)" within R.
> 
> The new image has updated drivers from Ubuntu the 12.04.2 release and so
> should work on some more modern computers.  I've not been able to test
> UEFI booting so if you have a UEFI machine you may need to set it back
> to BIOS boot for now.
> 
> The new STADEN Gap5 package and Taverna did not make this image release
> but will be coming soon.
> 
> Cheers,
> 
> TIM
> 
> -- 
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre 
> 
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB 
> 
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> 
> End of Bio-Linux Digest, Vol 59, Issue 4
> ****************************************



From tbooth at ceh.ac.uk  Thu Aug 15 13:43:05 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 15 Aug 2013 18:43:05 +0100
Subject: [Bio-Linux] RStudio with Bio-Linux
In-Reply-To: <E1685117-7357-4EC0-9A79-FD9D15859717@ohsu.edu>
References: <mailman.1.1374577201.16181.bio-linux@nebclists.nerc.ac.uk>
	<E1685117-7357-4EC0-9A79-FD9D15859717@ohsu.edu>
Message-ID: <1376588585.3416.211.camel@balisaur>

Hi Tom,

The RStudio website provides a .deb file which should work fine.  You
can fetch and install it from the command line like so:

wget http://download1.rstudio.org/rstudio-0.97.551-amd64.deb
sudo dpkg -i rstudio-0.97.551-amd64.deb
sudo apt-get -f install

The second command may report an error, but the third command fixes it.

Then open the dash and start typing "rstudio" and you should see the
icon, or just run "rstudio" on the command line.

Does that work for you?

Cheers,

TIM

On Thu, 2013-08-15 at 18:27 +0100, Tom Keller wrote:
> Hi Tim,
> Is there a way to use RStudio with R from Bio-Linux?
> 



From jeremy.she at biotec.or.th  Tue Aug 27 01:44:08 2013
From: jeremy.she at biotec.or.th (Jeremy Shearman)
Date: Tue, 27 Aug 2013 05:44:08 +0000
Subject: [Bio-Linux] please update tophat version
Message-ID: <5E8AFED5C97C894D8554A1D98682F90C3C561F@SPIMBN1B.biotec.or.th>

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

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-list/attachments/20130827/48bb2172/attachment.html>

From tbooth at ceh.ac.uk  Tue Aug 27 05:26:12 2013
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 27 Aug 2013 10:26:12 +0100
Subject: [Bio-Linux] please update tophat version
In-Reply-To: <5E8AFED5C97C894D8554A1D98682F90C3C561F@SPIMBN1B.biotec.or.th>
References: <5E8AFED5C97C894D8554A1D98682F90C3C561F@SPIMBN1B.biotec.or.th>
Message-ID: <1377595572.3416.426.camel@balisaur>

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
> 
> 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

-- 
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 thokeller at gmail.com  Tue Aug 27 12:45:34 2013
From: thokeller at gmail.com (Thomas Keller)
Date: Tue, 27 Aug 2013 09:45:34 -0700
Subject: [Bio-Linux] Bio-Linux Digest, Vol 60, Issue 1
In-Reply-To: <mailman.1.1376650801.13035.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1376650801.13035.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <1FB44C8F-CD02-4719-B46B-06F213891B41@gmail.com>

RStudio installed without error. 
Thanks!
   

 Tom
thokeller at gmail com



On Aug 16, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:

> Send Bio-Linux mailing list submissions to
> 	bio-linux at nebclists.nerc.ac.uk
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
> 	bio-linux-request at nebclists.nerc.ac.uk
> 
> You can reach the person managing the list at
> 	bio-linux-owner at nebclists.nerc.ac.uk
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: RStudio with Bio-Linux (Tom Keller)
>   2. Re: RStudio with Bio-Linux (Tim Booth)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 15 Aug 2013 10:27:13 -0700
> From: Tom Keller <kellert at ohsu.edu>
> Subject: Re: [Bio-Linux] RStudio with Bio-Linux
> To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> Message-ID: <E1685117-7357-4EC0-9A79-FD9D15859717 at ohsu.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Tim,
> Is there a way to use RStudio with R from Bio-Linux?
> 
> thanks for your help.
> Tom Keller
> Thomas J. Keller, Ph.D.; Director, DNA Services Core Facility ; Oregon Health & Science University;
> mailcode L220; 3181 SW Sam Jackson Park Rd; Portland, OR 97239; 503-494-2442
> 
> On Jul 23, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:
> 
>> Send Bio-Linux mailing list submissions to
>> 	bio-linux at nebclists.nerc.ac.uk
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>> or, via email, send a message with subject or body 'help' to
>> 	bio-linux-request at nebclists.nerc.ac.uk
>> 
>> You can reach the person managing the list at
>> 	bio-linux-owner at nebclists.nerc.ac.uk
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Bio-Linux digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Bio-Linux updated image and new packages (Tim Booth)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Mon, 22 Jul 2013 16:55:06 +0100
>> From: Tim Booth <tbooth at ceh.ac.uk>
>> Subject: [Bio-Linux] Bio-Linux updated image and new packages
>> To: Bio-Linux mailing list <bio-linux at nebclists.nerc.ac.uk>
>> Message-ID: <1374508506.10050.57.camel at balisaur>
>> Content-Type: text/plain; charset="UTF-8"
>> 
>> Hi All,
>> 
>> I've put a new Bio-Linux image update on the website today (7.0.7).
>> Existing users won't need to use this but I've added some new packages
>> which you might be interested in installing on your machines (sudo
>> apt-get install <packagename>):
>> 
>> abyss  (http://www.bcgsc.ca/platform/bioinfo/software/abyss)
>> ray    (http://denovoassembler.sourceforge.net/)
>> sickle (https://github.com/vsbuffalo/sickle)
>> scythe (https://github.com/vsbuffalo/scythe)
>> macs   (http://liulab.dfci.harvard.edu/MACS/)
>> 
>> The R environment has been upgraded to R3.0 and modules have been
>> recompiled to work on the new R.  If you have installed extra modules
>> and get an error about an incompatible R module you may need to run
>> "install.packages(<modulename>)" within R.
>> 
>> The new image has updated drivers from Ubuntu the 12.04.2 release and so
>> should work on some more modern computers.  I've not been able to test
>> UEFI booting so if you have a UEFI machine you may need to set it back
>> to BIOS boot for now.
>> 
>> The new STADEN Gap5 package and Taverna did not make this image release
>> but will be coming soon.
>> 
>> Cheers,
>> 
>> TIM
>> 
>> -- 
>> Tim Booth <tbooth at ceh.ac.uk>
>> NERC Environmental Bioinformatics Centre 
>> 
>> Centre for Ecology and Hydrology
>> Maclean Bldg, Benson Lane
>> Crowmarsh Gifford
>> Wallingford, England
>> OX10 8BB 
>> 
>> http://nebc.nerc.ac.uk
>> +44 1491 69 2705
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>> 
>> 
>> End of Bio-Linux Digest, Vol 59, Issue 4
>> ****************************************
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 15 Aug 2013 18:43:05 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> Subject: Re: [Bio-Linux] RStudio with Bio-Linux
> To: bio-linux at nebclists.nerc.ac.uk
> Message-ID: <1376588585.3416.211.camel at balisaur>
> Content-Type: text/plain; charset="UTF-8"
> 
> Hi Tom,
> 
> The RStudio website provides a .deb file which should work fine.  You
> can fetch and install it from the command line like so:
> 
> wget http://download1.rstudio.org/rstudio-0.97.551-amd64.deb
> sudo dpkg -i rstudio-0.97.551-amd64.deb
> sudo apt-get -f install
> 
> The second command may report an error, but the third command fixes it.
> 
> Then open the dash and start typing "rstudio" and you should see the
> icon, or just run "rstudio" on the command line.
> 
> Does that work for you?
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2013-08-15 at 18:27 +0100, Tom Keller wrote:
>> Hi Tim,
>> Is there a way to use RStudio with R from Bio-Linux?
>> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> 
> End of Bio-Linux Digest, Vol 60, Issue 1
> ****************************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-list/attachments/20130827/62d2ac94/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ic_list_big_grin.png
Type: image/png
Size: 1391 bytes
Desc: not available
URL: <http://www.bioinformatics.org/pipermail/bio-linux-list/attachments/20130827/62d2ac94/attachment.png>