From dksamuel2 at gmail.com  Tue Sep  1 05:01:27 2015
From: dksamuel2 at gmail.com (Duleep Samuel)
Date: Tue, 1 Sep 2015 14:31:27 +0530
Subject: [Bio-Linux] Portable biolinux not booting in Dell inspiron 3000
In-Reply-To: <CANj1AG2RbgT1ZVKFkexJB3dduv=sCm=fwOH4JdLRN+j9AtLN8A@mail.gmail.com>
References: <CANj1AG2RbgT1ZVKFkexJB3dduv=sCm=fwOH4JdLRN+j9AtLN8A@mail.gmail.com>
Message-ID: <CABqBg+D9RAXjAqYNWOyJYfKVJUmr1R6xBihzPWWbQ=x7AXwR8g@mail.gmail.com>

I would suggest that you use virtualbox and use biolinux, UEFI boot has
problems with Linux, Samuel, IIHR, Bangalore

On Fri, Aug 28, 2015 at 9:15 PM, Bishwa Kiran <kirannbishwa01 at gmail.com>
wrote:

> I have been trying to install a portable bio-linux OS on external hdd. I
> have followed the instructions given for portable ubuntu/bilinux
> installation which has been sucessful and also made sure the boot/grub
> loader is installed in the external harddrive (seagate 2 tb) during
> installation. After the completion of bio-linux installation it requests
> the restart and biolinux boots up. But, after the 2nd boot the boot widow
> of biolinux gives me an error (that a USB-3 port is not available or is
> offline). I have installed biolinux several times thinking the installation
> may have missed the files but it always turns out the same way- 1st restart
> works but after the second restart/boot there is an error message.
> My desktop is Dell inspiron 3000 (i3) which by default uses UEFI boot
> system and I have disabled it while preparing the biolinux installation and
> have used legacy mode (modified BIOS setting).
> One interesting thing is that the same portable biolinux OS which didn't
> boot from desktop boots from my gateway laptop every time though. So, the
> problem basically is that the USB-3 port is not getting recognized while
> booting. I tried another USB-3 port which gave same error, all other  USB 2
> port however show biolinux OS loading (shows a loading Biolinux logo) but
> never fully boots even after 2-3 hours.
>
> I have been trying to make this work for 5 days now. I need to use this
> portable OS mainly on my desktop due it its higher performance and also I
> have to keep things running overnight.
> Any suggestions appreciated and thanks in advance.
>
> I took the picture of the error message.
>
>
> --
> - Bish
>
>
>
> _______________________________________________
> 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  Tue Sep  1 07:41:38 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 01 Sep 2015 12:41:38 +0100
Subject: [Bio-Linux] Portable biolinux not booting in Dell inspiron 3000
In-Reply-To: <CABqBg+D9RAXjAqYNWOyJYfKVJUmr1R6xBihzPWWbQ=x7AXwR8g@mail.gmail.com>
References: <CANj1AG2RbgT1ZVKFkexJB3dduv=sCm=fwOH4JdLRN+j9AtLN8A@mail.gmail.com>
 <CABqBg+D9RAXjAqYNWOyJYfKVJUmr1R6xBihzPWWbQ=x7AXwR8g@mail.gmail.com>
Message-ID: <1441107698.5600.56.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Bish,

Your image of the error seems to have been eaten by the mailing list
server.  Could you please paste it onto pasteboard.co (or somewhere
similar) and send the link?

There can be issues with UEFI and Linux but this is normally because of
flaky UEFI implementations and Dells should behave themselves so I think
it should be possible to achieve what you want and get it to boot
reliably.  From your description I can't tell if the error regarding
USB-3 is coming from Grub or from the Kernel.  Hopefully when I see the
screenshot image it will be clear.

Once I can see where in the boot process the error is occurring I think
we can use the Gateway laptop to fix the system on the drive.  If you
plug the external drive into your Gateway it boots right up, right?  If
so, things we can do are:

1) Disable the boot logo and reveal all the diagnostic messages
2) Force Grub to load all relevant drivers
3) Rebuild the initrd to ensure the kernel properly starts the USB3
stack before mounting the root filesystem
4) Upgrade the kernel to the "utopic" or "vivid" backport version.  I
can't do this on the regular ISO because it stuffs up VirtualBox client
driver support, but it might well fix your problem.

Anyway, post up the image and we'll go from there.

Cheers,

TIM

On Tue, 2015-09-01 at 14:31 +0530, Duleep Samuel wrote:
> I would suggest that you use virtualbox and use biolinux, UEFI boot
> has problems with Linux, Samuel, IIHR, Bangalore
> 
> On Fri, Aug 28, 2015 at 9:15 PM, Bishwa Kiran
> <kirannbishwa01 at gmail.com> wrote:
>         I have been trying to install a portable bio-linux OS on
>         external hdd. I have followed the instructions given for
>         portable ubuntu/bilinux installation which has been sucessful
>         and also made sure the boot/grub loader is installed in the
>         external harddrive (seagate 2 tb) during installation. After
>         the completion of bio-linux installation it requests the
>         restart and biolinux boots up. But, after the 2nd boot the
>         boot widow of biolinux gives me an error (that a USB-3 port is
>         not available or is offline). I have installed biolinux
>         several times thinking the installation may have missed the
>         files but it always turns out the same way- 1st restart works
>         but after the second restart/boot there is an error message.
>         My desktop is Dell inspiron 3000 (i3) which by default uses
>         UEFI boot system and I have disabled it while preparing the
>         biolinux installation and have used legacy mode (modified BIOS
>         setting).
>         One interesting thing is that the same portable biolinux OS
>         which didn't boot from desktop boots from my gateway laptop
>         every time though. So, the problem basically is that the USB-3
>         port is not getting recognized while booting. I tried another
>         USB-3 port which gave same error, all other  USB 2 port
>         however show biolinux OS loading (shows a loading Biolinux
>         logo) but never fully boots even after 2-3 hours.
>         
>         
>         I have been trying to make this work for 5 days now. I need to
>         use this portable OS mainly on my desktop due it its higher
>         performance and also I have to keep things running overnight.
>         Any suggestions appreciated and thanks in advance.
>         
>         
>         I took the picture of the error message.
>         
>         
>         -- 
>         - Bish     
>          
>         
>          
>         
>         _______________________________________________
>         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>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From tbooth at ceh.ac.uk  Tue Sep  1 11:54:51 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 01 Sep 2015 16:54:51 +0100
Subject: [Bio-Linux] tophat with -p > 1 results in missing reads
In-Reply-To: <55D76470.2030106@rci.rutgers.edu>
References: <55D76470.2030106@rci.rutgers.edu>
Message-ID: <1441122891.5600.68.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

Tophat and Bowtie and Bowtie2 are now fully up-to-date.  Sorry this took
a while - I've had holidays and interviews and grant proposal deadlines
to deal with.

I see there was no response to the GitHub bug report yet.  Maybe the
developers are on hols too.

TIM

On Fri, 2015-08-21 at 13:48 -0400, Josh Thackray wrote:
> Hi All,
> 
> I am running tophat (version 2.0.13, from the biolinux distribution). I 
> am facing a problem where running tophat with increasing values for -p 
> (number of threads) results in more and more reads lost in the final 
> output. I'm starting with an uncompressed fastq file containing  
> 18,115,321 reads, and running tophat with default parameters except for 
> -p and -o.
> 
> Running -p 8 results with the following information in align_summary.txt:
>      Input     :    318640
>      Mapped:    191949 (60.2% of input)
>      of these:     29316 (15.3%) have multiple alignments (0 have >20)
>      60.2% overall read mapping rate.
> 
> Running -p 4 results with the following information in align_summary.txt:
>      Input     :   1302700
>      Mapped:     759998 (58.3% of input)
>      of these:     115861 (15.2%) have multiple alignments (1 have >20)
>      58.3% overall read mapping rate.
> 
> Running -p 1 results with the following information in align_summary.txt:
>      Input     :  18115321
>      Mapped:  12014534 (66.3% of input)
>      of these:   1867188 (15.5%) have multiple alignments (13 have >20)
>      66.3% overall read mapping rate.
> 
> I also tried running tophat with the --no-sort-bam option to check if 
> samtools was somehow screwing up during the mergesort operation, but I 
> get the same result. I also confirmed the numbers reported in the 
> align_summary.txt file using the samtools flagstat command. Further 
> using bowtie1 instead of bowtie2 for the alignment engine did not 
> resolve the problem of these reads going missing.
> 
> Any ideas???
> 
> Thanks,
> 
> Josh
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From tbooth at ceh.ac.uk  Thu Sep  3 13:16:21 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 03 Sep 2015 18:16:21 +0100
Subject: [Bio-Linux] tophat 2.0.13 missing reads
In-Reply-To: <55D76470.2030106@rci.rutgers.edu>
References: <55D76470.2030106@rci.rutgers.edu>
Message-ID: <1441300581.5600.170.camel@wllt1771.nerc-wallingford.ac.uk>

Hi All,

I just wanted to report back to this list that there was, indeed, an
issue with Tophat 2.0.13 which was on Bio-Linux since December last
year.

See comments from @gpertea on
https://github.com/infphilo/tophat/issues/18

So if you have used Tophat for something this year you should consider
re-running the alignment with the new updated version to check your
results, even if you did not use multi-thread mode.

Best,

TIM

On Fri, 2015-08-21 at 13:48 -0400, Josh Thackray wrote:
> Hi All,
> 
> I am running tophat (version 2.0.13, from the biolinux distribution). I 
> am facing a problem where running tophat with increasing values for -p 
> (number of threads) results in more and more reads lost in the final 
> output. I'm starting with an uncompressed fastq file containing  
> 18,115,321 reads, and running tophat with default parameters except for 
> -p and -o.
> 
> Running -p 8 results with the following information in align_summary.txt:
>      Input     :    318640
>      Mapped:    191949 (60.2% of input)
>      of these:     29316 (15.3%) have multiple alignments (0 have >20)
>      60.2% overall read mapping rate.
> 
> Running -p 4 results with the following information in align_summary.txt:
>      Input     :   1302700
>      Mapped:     759998 (58.3% of input)
>      of these:     115861 (15.2%) have multiple alignments (1 have >20)
>      58.3% overall read mapping rate.
> 
> Running -p 1 results with the following information in align_summary.txt:
>      Input     :  18115321
>      Mapped:  12014534 (66.3% of input)
>      of these:   1867188 (15.5%) have multiple alignments (13 have >20)
>      66.3% overall read mapping rate.
> 
> I also tried running tophat with the --no-sort-bam option to check if 
> samtools was somehow screwing up during the mergesort operation, but I 
> get the same result. I also confirmed the numbers reported in the 
> align_summary.txt file using the samtools flagstat command. Further 
> using bowtie1 instead of bowtie2 for the alignment engine did not 
> resolve the problem of these reads going missing.
> 
> Any ideas???
> 
> Thanks,
> 
> Josh
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From thackray at rci.rutgers.edu  Thu Sep  3 13:39:29 2015
From: thackray at rci.rutgers.edu (Josh Thackray)
Date: Thu, 3 Sep 2015 13:39:29 -0400
Subject: [Bio-Linux] tophat with -p > 1 results in missing reads
In-Reply-To: <mailman.1.1441191602.17651.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1441191602.17651.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <55E885D1.3070401@rci.rutgers.edu>

Hi Tim,

As I posted on the tophat github issue tracker 
(https://github.com/infphilo/tophat/issues/18), it looks like the 
upgrade solved the problems I was having. Thanks very much for your help!

Just as an aside, I don't receive replies to my messages on the email 
list (though I do receive the digest emails). Is there any way to fix this?

Thanks,

Josh

Josh Thackray
Laboratory Researcher III
Human Genetics Institute of NJ
Department of Genetics
Rutgers University

On 9/2/2015 7:00 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: Portable biolinux not booting in Dell inspiron 3000
>        (Tim Booth)
>     2. Re: tophat with -p > 1 results in missing reads (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 01 Sep 2015 12:41:38 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Portable biolinux not booting in Dell
> 	inspiron 3000
> Message-ID: <1441107698.5600.56.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Bish,
>
> Your image of the error seems to have been eaten by the mailing list
> server.  Could you please paste it onto pasteboard.co (or somewhere
> similar) and send the link?
>
> There can be issues with UEFI and Linux but this is normally because of
> flaky UEFI implementations and Dells should behave themselves so I think
> it should be possible to achieve what you want and get it to boot
> reliably.  From your description I can't tell if the error regarding
> USB-3 is coming from Grub or from the Kernel.  Hopefully when I see the
> screenshot image it will be clear.
>
> Once I can see where in the boot process the error is occurring I think
> we can use the Gateway laptop to fix the system on the drive.  If you
> plug the external drive into your Gateway it boots right up, right?  If
> so, things we can do are:
>
> 1) Disable the boot logo and reveal all the diagnostic messages
> 2) Force Grub to load all relevant drivers
> 3) Rebuild the initrd to ensure the kernel properly starts the USB3
> stack before mounting the root filesystem
> 4) Upgrade the kernel to the "utopic" or "vivid" backport version.  I
> can't do this on the regular ISO because it stuffs up VirtualBox client
> driver support, but it might well fix your problem.
>
> Anyway, post up the image and we'll go from there.
>
> Cheers,
>
> TIM
>
> On Tue, 2015-09-01 at 14:31 +0530, Duleep Samuel wrote:
>> I would suggest that you use virtualbox and use biolinux, UEFI boot
>> has problems with Linux, Samuel, IIHR, Bangalore
>>
>> On Fri, Aug 28, 2015 at 9:15 PM, Bishwa Kiran
>> <kirannbishwa01 at gmail.com> wrote:
>>          I have been trying to install a portable bio-linux OS on
>>          external hdd. I have followed the instructions given for
>>          portable ubuntu/bilinux installation which has been sucessful
>>          and also made sure the boot/grub loader is installed in the
>>          external harddrive (seagate 2 tb) during installation. After
>>          the completion of bio-linux installation it requests the
>>          restart and biolinux boots up. But, after the 2nd boot the
>>          boot widow of biolinux gives me an error (that a USB-3 port is
>>          not available or is offline). I have installed biolinux
>>          several times thinking the installation may have missed the
>>          files but it always turns out the same way- 1st restart works
>>          but after the second restart/boot there is an error message.
>>          My desktop is Dell inspiron 3000 (i3) which by default uses
>>          UEFI boot system and I have disabled it while preparing the
>>          biolinux installation and have used legacy mode (modified BIOS
>>          setting).
>>          One interesting thing is that the same portable biolinux OS
>>          which didn't boot from desktop boots from my gateway laptop
>>          every time though. So, the problem basically is that the USB-3
>>          port is not getting recognized while booting. I tried another
>>          USB-3 port which gave same error, all other  USB 2 port
>>          however show biolinux OS loading (shows a loading Biolinux
>>          logo) but never fully boots even after 2-3 hours.
>>          
>>          
>>          I have been trying to make this work for 5 days now. I need to
>>          use this portable OS mainly on my desktop due it its higher
>>          performance and also I have to keep things running overnight.
>>          Any suggestions appreciated and thanks in advance.
>>          
>>          
>>          I took the picture of the error message.
>>          
>>          
>>          --
>>          - Bish
>>           
>>          
>>           
>>          
>>          _______________________________________________
>>          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



From tbooth at ceh.ac.uk  Mon Sep 14 06:42:46 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 14 Sep 2015 11:42:46 +0100
Subject: [Bio-Linux] Trinity added, Mothur and Mira updated
Message-ID: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>

Hi All,

I've been doing a round of package updates on Bio-Linux 8 over the last
week.  We now have both Mothur and Mira updated to the latest versions:

mira-assembler package is version 4.9.5
mothur package is version 1.36.1

Both will be updated by the package updater. If you experience any
problems or regressions with these new packages please let me know.

I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
been added to the package repository (http://trinityrnaseq.github.io/).
Various modifications have been made to Trinity to make it integrate
nicely with the other packages on the system, so if you have problems
running it please let me know and I'll check if it is maybe something
that got messed up in the packaging.

trinityrnaseq package is version 2.0.6

To get it: sudo apt-get install trinityrnaseq
then just type: "Trinity" (with the capital T)

The credit for all this goes mainly to Michael and Andreas from the
Debian Med project who maintain these packages in Debian.  I've been
able to take what they made and backport it to Bio-Linux for you.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From briancady101 at yahoo.com  Mon Sep 14 07:25:46 2015
From: briancady101 at yahoo.com (Brian Cady)
Date: Mon, 14 Sep 2015 11:25:46 +0000 (UTC)
Subject: [Bio-Linux] Trinity added, Mothur and Mira updated
In-Reply-To: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <1221772328.2194448.1442229946620.JavaMail.yahoo@mail.yahoo.com>

Tim Booth, thank you for what you do,I use Bio-Linux daily, yet only use a small fraction of its capabilities.
Brian
 


     On Monday, September 14, 2015 6:42 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
   

 Hi All,

I've been doing a round of package updates on Bio-Linux 8 over the last
week.? We now have both Mothur and Mira updated to the latest versions:

mira-assembler package is version 4.9.5
mothur package is version 1.36.1

Both will be updated by the package updater. If you experience any
problems or regressions with these new packages please let me know.

I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
been added to the package repository (http://trinityrnaseq.github.io/).
Various modifications have been made to Trinity to make it integrate
nicely with the other packages on the system, so if you have problems
running it please let me know and I'll check if it is maybe something
that got messed up in the packaging.

trinityrnaseq package is version 2.0.6

To get it: sudo apt-get install trinityrnaseq
then just type: "Trinity" (with the capital T)

The credit for all this goes mainly to Michael and Andreas from the
Debian Med project who maintain these packages in Debian.? I've been
able to take what they made and backport it to Bio-Linux for you.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297


_______________________________________________
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 paumarc at gmail.com  Mon Sep 14 08:01:12 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Mon, 14 Sep 2015 14:01:12 +0200
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <CADFuJLhavnBkOpiC675fZCrwO1yOUTpm5jnwttP3cZJ_z7s4Aw@mail.gmail.com>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
 <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
 <CADFuJLhavnBkOpiC675fZCrwO1yOUTpm5jnwttP3cZJ_z7s4Aw@mail.gmail.com>
Message-ID: <CADFuJLgqeGS6ysbUqDXYN0JF+5VcQnUJK-mLy0XieNzMKMb5Fg@mail.gmail.com>

Hello everybody

 I still trying to work with Rapidr package from R. As someone pointed in a
mail, I think it was Dr Tony Travis, it uses some packages that have
changed recently. I thought I could deal with this installing the R package
GenomicAlignments version 1.14.4 locally. Unfortunately, the compilation of
the package failed. I have been thinking on install biolinux 7 in another
computer, but I not sure if it would work. Could you tell me which version
of the package is in biolinux 7? I amb not worried about biolinux
actualizacions as long as it only will be used to run this programs

thanks

pau

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/


2015-06-19 16:59 GMT+02:00 Pau Marc Mu?oz Torres <paumarc at gmail.com>:

> Thanks
>
> P
> El 19/06/2015 13:19, "Tim Booth" <tbooth at ceh.ac.uk> escribi?:
>
>> Hi Pau Marc,
>>
>> On Bio-Linux 8 you can install all packages from the big auto-generated
>> C2D4U repository via apt-get, so for example you can do:
>>
>> apt-get install r-bioc-genomicalignments
>>
>> However, RAPIDR is missing, so for now you have to install it via
>> install.packages() and update it manually as Tony suggested.
>>
>> I'll look into adding a package for this myself.  Its normally very easy
>> to do.
>>
>> Cheers,
>>
>> TIM
>>
>> On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:
>> > On 19/06/15 11:04, Pau Marc Mu?oz Torres wrote:
>> > > Hello9 everybody.
>> > >
>> > >  I'm, interested to install R-cran package on my system, nevertheless
>> i
>> > > do not find it at repositories neither in bioconductor
>> > >
>> > > i look at R-cram web page for Rapidir , and i have not found any linux
>> > > binary.
>> > >
>> > > http://cran.r-project.org/web/packages/RAPIDR/index.html
>> > >
>> > > Can some one told me if it is possible to install it in  biolinux?
>> >
>> > Hi, Pau Marc.
>> >
>> > The CRAN package "RAPIDR" requires a BioConductor package
>> > "GenomicAlignments", which must be installed first. See:
>> >
>> > > http://cran.r-project.org/web/packages/RAPIDR/index.html
>> > >
>> http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
>> >
>> > This is how to install and load "RAPIDR" in Bio-Linux 8:
>> >
>> >   R
>> >   source("http://bioconductor.org/biocLite.R")
>> >   biocLite("GenomicAlignments")
>> >   install.packages("RAPIDR")
>> >   library(RAPIDR)
>> >
>> > HTH,
>> >
>> >   Tony.
>> >
>>
>> --
>> Tim Booth <tbooth at ceh.ac.uk>
>>
>> Centre for Ecology and Hydrology
>> Maclean Bldg, Benson Lane
>> Crowmarsh Gifford
>> Wallingford, England
>> OX10 8BB
>>
>> http://environmentalomics.org/bio-linux
>> +44 1491 69 2297
>>
>>
>> _______________________________________________
>> 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 kirannbishwa01 at gmail.com  Mon Sep 14 09:00:23 2015
From: kirannbishwa01 at gmail.com (Bishwa Kiran)
Date: Mon, 14 Sep 2015 09:00:23 -0400
Subject: [Bio-Linux] Trinity added, Mothur and Mira updated
In-Reply-To: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>

Thanks for the update !

On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi All,
>
> I've been doing a round of package updates on Bio-Linux 8 over the last
> week.  We now have both Mothur and Mira updated to the latest versions:
>
> mira-assembler package is version 4.9.5
> mothur package is version 1.36.1
>
> Both will be updated by the package updater. If you experience any
> problems or regressions with these new packages please let me know.
>
> I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
> been added to the package repository (http://trinityrnaseq.github.io/).
> Various modifications have been made to Trinity to make it integrate
> nicely with the other packages on the system, so if you have problems
> running it please let me know and I'll check if it is maybe something
> that got messed up in the packaging.
>
> trinityrnaseq package is version 2.0.6
>
> To get it: sudo apt-get install trinityrnaseq
> then just type: "Trinity" (with the capital T)
>
> The credit for all this goes mainly to Michael and Andreas from the
> Debian Med project who maintain these packages in Debian.  I've been
> able to take what they made and backport it to Bio-Linux for you.
>
> Cheers,
>
> TIM
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>



-- 
- Bish
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From tbooth at ceh.ac.uk  Mon Sep 14 09:41:09 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 14 Sep 2015 14:41:09 +0100
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <CADFuJLgqeGS6ysbUqDXYN0JF+5VcQnUJK-mLy0XieNzMKMb5Fg@mail.gmail.com>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
 <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
 <CADFuJLhavnBkOpiC675fZCrwO1yOUTpm5jnwttP3cZJ_z7s4Aw@mail.gmail.com>
 <CADFuJLgqeGS6ysbUqDXYN0JF+5VcQnUJK-mLy0XieNzMKMb5Fg@mail.gmail.com>
Message-ID: <1442238069.32554.21.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

I honestly don't know if RapidR will install cleanly on BL7.  However, I
would direct you to
http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova which is a BL7
image you can import in VirtualBox, which will be much quicker than
installing it on bare metal.  Note the admin account is manager,
password also manager.

I'll have another look at the package.  I'd assumed before that you
could install it easily via install.packages() but if it's problematic
then it's more worth my time to fix it for everyone.

Cheers,

TIM

On Mon, 2015-09-14 at 14:01 +0200, Pau Marc Mu?oz Torres wrote:
> Hello everybody
> 
> 
>  I still trying to work with Rapidr package from R. As someone pointed
> in a mail, I think it was Dr Tony Travis, it uses some packages that
> have changed recently. I thought I could deal with this installing the
> R package GenomicAlignments version 1.14.4 locally. Unfortunately, the
> compilation of the package failed. I have been thinking on install
> biolinux 7 in another computer, but I not sure if it would work. Could
> you tell me which version of the package is in biolinux 7? I amb not
> worried about biolinux actualizacions as long as it only will be used
> to run this programs
> 
> 
> thanks
> 
> 
> pau
> 
> Pau Marc Mu?oz Torres
> 
> skype: pau_marc
> http://www.linkedin.com/in/paumarc
> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
> 
> 
> 
> 2015-06-19 16:59 GMT+02:00 Pau Marc Mu?oz Torres <paumarc at gmail.com>:
>         Thanks
>         
>         P
>         
>         El 19/06/2015 13:19, "Tim Booth" <tbooth at ceh.ac.uk> escribi?:
>                 Hi Pau Marc,
>                 
>                 On Bio-Linux 8 you can install all packages from the
>                 big auto-generated
>                 C2D4U repository via apt-get, so for example you can
>                 do:
>                 
>                 apt-get install r-bioc-genomicalignments
>                 
>                 However, RAPIDR is missing, so for now you have to
>                 install it via
>                 install.packages() and update it manually as Tony
>                 suggested.
>                 
>                 I'll look into adding a package for this myself.  Its
>                 normally very easy
>                 to do.
>                 
>                 Cheers,
>                 
>                 TIM
>                 
>                 On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:
>                 > On 19/06/15 11:04, Pau Marc Mu?oz Torres wrote:
>                 > > Hello9 everybody.
>                 > >
>                 > >  I'm, interested to install R-cran package on my
>                 system, nevertheless i
>                 > > do not find it at repositories neither in
>                 bioconductor
>                 > >
>                 > > i look at R-cram web page for Rapidir , and i have
>                 not found any linux
>                 > > binary.
>                 > >
>                 > >
>                 http://cran.r-project.org/web/packages/RAPIDR/index.html
>                 > >
>                 > > Can some one told me if it is possible to install
>                 it in  biolinux?
>                 >
>                 > Hi, Pau Marc.
>                 >
>                 > The CRAN package "RAPIDR" requires a BioConductor
>                 package
>                 > "GenomicAlignments", which must be installed first.
>                 See:
>                 >
>                 > >
>                 http://cran.r-project.org/web/packages/RAPIDR/index.html
>                 > >
>                 http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
>                 >
>                 > This is how to install and load "RAPIDR" in
>                 Bio-Linux 8:
>                 >
>                 >   R
>                 >   source("http://bioconductor.org/biocLite.R")
>                 >   biocLite("GenomicAlignments")
>                 >   install.packages("RAPIDR")
>                 >   library(RAPIDR)
>                 >
>                 > HTH,
>                 >
>                 >   Tony.
>                 >
>                 
>                 --
>                 Tim Booth <tbooth at ceh.ac.uk>
>                 
>                 Centre for Ecology and Hydrology
>                 Maclean Bldg, Benson Lane
>                 Crowmarsh Gifford
>                 Wallingford, England
>                 OX10 8BB
>                 
>                 http://environmentalomics.org/bio-linux
>                 +44 1491 69 2297
>                 
>                 
>                 _______________________________________________
>                 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>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From paumarc at gmail.com  Tue Sep 15 04:24:06 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Tue, 15 Sep 2015 10:24:06 +0200
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <1442238069.32554.21.camel@wllt1771.nerc-wallingford.ac.uk>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
 <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
 <CADFuJLhavnBkOpiC675fZCrwO1yOUTpm5jnwttP3cZJ_z7s4Aw@mail.gmail.com>
 <CADFuJLgqeGS6ysbUqDXYN0JF+5VcQnUJK-mLy0XieNzMKMb5Fg@mail.gmail.com>
 <1442238069.32554.21.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CADFuJLhS=V93vZbOmCQ2Nu+SuRTAH_M_JHOorxApX3=1Oj4bPQ@mail.gmail.com>

Hi Tim,

 Thanks for your answer. I am trying to download the link but i can't
connect to it

http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova

pau


Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/


2015-09-14 15:41 GMT+02:00 Tim Booth <tbooth at ceh.ac.uk>:

> Hi,
>
> I honestly don't know if RapidR will install cleanly on BL7.  However, I
> would direct you to
> http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova which is a BL7
> image you can import in VirtualBox, which will be much quicker than
> installing it on bare metal.  Note the admin account is manager,
> password also manager.
>
> I'll have another look at the package.  I'd assumed before that you
> could install it easily via install.packages() but if it's problematic
> then it's more worth my time to fix it for everyone.
>
> Cheers,
>
> TIM
>
> On Mon, 2015-09-14 at 14:01 +0200, Pau Marc Mu?oz Torres wrote:
> > Hello everybody
> >
> >
> >  I still trying to work with Rapidr package from R. As someone pointed
> > in a mail, I think it was Dr Tony Travis, it uses some packages that
> > have changed recently. I thought I could deal with this installing the
> > R package GenomicAlignments version 1.14.4 locally. Unfortunately, the
> > compilation of the package failed. I have been thinking on install
> > biolinux 7 in another computer, but I not sure if it would work. Could
> > you tell me which version of the package is in biolinux 7? I amb not
> > worried about biolinux actualizacions as long as it only will be used
> > to run this programs
> >
> >
> > thanks
> >
> >
> > pau
> >
> > Pau Marc Mu?oz Torres
> >
> > skype: pau_marc
> > http://www.linkedin.com/in/paumarc
> > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
> >
> >
> >
> > 2015-06-19 16:59 GMT+02:00 Pau Marc Mu?oz Torres <paumarc at gmail.com>:
> >         Thanks
> >
> >         P
> >
> >         El 19/06/2015 13:19, "Tim Booth" <tbooth at ceh.ac.uk> escribi?:
> >                 Hi Pau Marc,
> >
> >                 On Bio-Linux 8 you can install all packages from the
> >                 big auto-generated
> >                 C2D4U repository via apt-get, so for example you can
> >                 do:
> >
> >                 apt-get install r-bioc-genomicalignments
> >
> >                 However, RAPIDR is missing, so for now you have to
> >                 install it via
> >                 install.packages() and update it manually as Tony
> >                 suggested.
> >
> >                 I'll look into adding a package for this myself.  Its
> >                 normally very easy
> >                 to do.
> >
> >                 Cheers,
> >
> >                 TIM
> >
> >                 On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:
> >                 > On 19/06/15 11:04, Pau Marc Mu?oz Torres wrote:
> >                 > > Hello9 everybody.
> >                 > >
> >                 > >  I'm, interested to install R-cran package on my
> >                 system, nevertheless i
> >                 > > do not find it at repositories neither in
> >                 bioconductor
> >                 > >
> >                 > > i look at R-cram web page for Rapidir , and i have
> >                 not found any linux
> >                 > > binary.
> >                 > >
> >                 > >
> >                 http://cran.r-project.org/web/packages/RAPIDR/index.html
> >                 > >
> >                 > > Can some one told me if it is possible to install
> >                 it in  biolinux?
> >                 >
> >                 > Hi, Pau Marc.
> >                 >
> >                 > The CRAN package "RAPIDR" requires a BioConductor
> >                 package
> >                 > "GenomicAlignments", which must be installed first.
> >                 See:
> >                 >
> >                 > >
> >                 http://cran.r-project.org/web/packages/RAPIDR/index.html
> >                 > >
> >
> http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
> >                 >
> >                 > This is how to install and load "RAPIDR" in
> >                 Bio-Linux 8:
> >                 >
> >                 >   R
> >                 >   source("http://bioconductor.org/biocLite.R")
> >                 >   biocLite("GenomicAlignments")
> >                 >   install.packages("RAPIDR")
> >                 >   library(RAPIDR)
> >                 >
> >                 > HTH,
> >                 >
> >                 >   Tony.
> >                 >
> >
> >                 --
> >                 Tim Booth <tbooth at ceh.ac.uk>
> >
> >                 Centre for Ecology and Hydrology
> >                 Maclean Bldg, Benson Lane
> >                 Crowmarsh Gifford
> >                 Wallingford, England
> >                 OX10 8BB
> >
> >                 http://environmentalomics.org/bio-linux
> >                 +44 1491 69 2297
> >
> >
> >                 _______________________________________________
> >                 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>
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
> _______________________________________________
> 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  Tue Sep 15 14:09:26 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 15 Sep 2015 19:09:26 +0100
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <CADFuJLhS=V93vZbOmCQ2Nu+SuRTAH_M_JHOorxApX3=1Oj4bPQ@mail.gmail.com>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
 <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
 <CADFuJLhavnBkOpiC675fZCrwO1yOUTpm5jnwttP3cZJ_z7s4Aw@mail.gmail.com>
 <CADFuJLgqeGS6ysbUqDXYN0JF+5VcQnUJK-mLy0XieNzMKMb5Fg@mail.gmail.com>
 <1442238069.32554.21.camel@wllt1771.nerc-wallingford.ac.uk>
 <CADFuJLhS=V93vZbOmCQ2Nu+SuRTAH_M_JHOorxApX3=1Oj4bPQ@mail.gmail.com>
Message-ID: <1442340566.32554.105.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Pau,

I did a bunch of Bioconductor package updates and tried making a RAPIDR
package for Bio-Linux 8.  I checked that it loads into R, but can you
try it and see if it actually works?

$ sudo apt-get install r-cran-rapidr
...
$ R
...
> library(RAPIDR)
Creating a generic function for ?nchar? from package ?base? in package
?S4Vectors?
>

So there is a warning message.  Hopefully not a problem.

If it doesn't work, what errors do you get?

For the download link, that link is good but you could also try the
mirror site:

http://ftp.yzu.edu.tw/Linux/bio-linux-iso/bio-linux-7-20131211.ova

Cheers,

TIM

On Tue, 2015-09-15 at 10:24 +0200, Pau Marc Mu?oz Torres wrote:
> Hi Tim,
> 
> 
>  Thanks for your answer. I am trying to download the link but i can't
> connect to it
> 
> 
> http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova
> 
> 
> 
> pau
>  
> 
> Pau Marc Mu?oz Torres
> 
> skype: pau_marc
> http://www.linkedin.com/in/paumarc
> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
> 
> 
> 
> 2015-09-14 15:41 GMT+02:00 Tim Booth <tbooth at ceh.ac.uk>:
>         Hi,
>         
>         I honestly don't know if RapidR will install cleanly on BL7.
>         However, I
>         would direct you to
>         http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova
>         which is a BL7
>         image you can import in VirtualBox, which will be much quicker
>         than
>         installing it on bare metal.  Note the admin account is
>         manager,
>         password also manager.
>         
>         I'll have another look at the package.  I'd assumed before
>         that you
>         could install it easily via install.packages() but if it's
>         problematic
>         then it's more worth my time to fix it for everyone.
>         
>         Cheers,
>         
>         TIM
>         
>         On Mon, 2015-09-14 at 14:01 +0200, Pau Marc Mu?oz Torres
>         wrote:
>         > Hello everybody
>         >
>         >
>         >  I still trying to work with Rapidr package from R. As
>         someone pointed
>         > in a mail, I think it was Dr Tony Travis, it uses some
>         packages that
>         > have changed recently. I thought I could deal with this
>         installing the
>         > R package GenomicAlignments version 1.14.4 locally.
>         Unfortunately, the
>         > compilation of the package failed. I have been thinking on
>         install
>         > biolinux 7 in another computer, but I not sure if it would
>         work. Could
>         > you tell me which version of the package is in biolinux 7? I
>         amb not
>         > worried about biolinux actualizacions as long as it only
>         will be used
>         > to run this programs
>         >
>         >
>         > thanks
>         >
>         >
>         > pau
>         >
>         > Pau Marc Mu?oz Torres
>         >
>         > skype: pau_marc
>         > http://www.linkedin.com/in/paumarc
>         > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
>         >
>         >
>         >
>         > 2015-06-19 16:59 GMT+02:00 Pau Marc Mu?oz Torres
>         <paumarc at gmail.com>:
>         >         Thanks
>         >
>         >         P
>         >
>         >         El 19/06/2015 13:19, "Tim Booth" <tbooth at ceh.ac.uk>
>         escribi?:
>         >                 Hi Pau Marc,
>         >
>         >                 On Bio-Linux 8 you can install all packages
>         from the
>         >                 big auto-generated
>         >                 C2D4U repository via apt-get, so for example
>         you can
>         >                 do:
>         >
>         >                 apt-get install r-bioc-genomicalignments
>         >
>         >                 However, RAPIDR is missing, so for now you
>         have to
>         >                 install it via
>         >                 install.packages() and update it manually as
>         Tony
>         >                 suggested.
>         >
>         >                 I'll look into adding a package for this
>         myself.  Its
>         >                 normally very easy
>         >                 to do.
>         >
>         >                 Cheers,
>         >
>         >                 TIM
>         >
>         >                 On Fri, 2015-06-19 at 11:41 +0100, Tony
>         Travis wrote:
>         >                 > On 19/06/15 11:04, Pau Marc Mu?oz Torres
>         wrote:
>         >                 > > Hello9 everybody.
>         >                 > >
>         >                 > >  I'm, interested to install R-cran
>         package on my
>         >                 system, nevertheless i
>         >                 > > do not find it at repositories neither
>         in
>         >                 bioconductor
>         >                 > >
>         >                 > > i look at R-cram web page for Rapidir ,
>         and i have
>         >                 not found any linux
>         >                 > > binary.
>         >                 > >
>         >                 > >
>         >
>          http://cran.r-project.org/web/packages/RAPIDR/index.html
>         >                 > >
>         >                 > > Can some one told me if it is possible
>         to install
>         >                 it in  biolinux?
>         >                 >
>         >                 > Hi, Pau Marc.
>         >                 >
>         >                 > The CRAN package "RAPIDR" requires a
>         BioConductor
>         >                 package
>         >                 > "GenomicAlignments", which must be
>         installed first.
>         >                 See:
>         >                 >
>         >                 > >
>         >
>          http://cran.r-project.org/web/packages/RAPIDR/index.html
>         >                 > >
>         >
>          http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
>         >                 >
>         >                 > This is how to install and load "RAPIDR"
>         in
>         >                 Bio-Linux 8:
>         >                 >
>         >                 >   R
>         >                 >
>          source("http://bioconductor.org/biocLite.R")
>         >                 >   biocLite("GenomicAlignments")
>         >                 >   install.packages("RAPIDR")
>         >                 >   library(RAPIDR)
>         >                 >
>         >                 > HTH,
>         >                 >
>         >                 >   Tony.
>         >                 >
>         >
>         >                 --
>         >                 Tim Booth <tbooth at ceh.ac.uk>
>         >
>         >                 Centre for Ecology and Hydrology
>         >                 Maclean Bldg, Benson Lane
>         >                 Crowmarsh Gifford
>         >                 Wallingford, England
>         >                 OX10 8BB
>         >
>         >                 http://environmentalomics.org/bio-linux
>         >                 +44 1491 69 2297
>         >
>         >
>         >
>          _______________________________________________
>         >                 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>
>         
>         Centre for Ecology and Hydrology
>         Maclean Bldg, Benson Lane
>         Crowmarsh Gifford
>         Wallingford, England
>         OX10 8BB
>         
>         http://environmentalomics.org/bio-linux
>         +44 1491 69 2297
>         
>         
>         _______________________________________________
>         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>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From tbooth at ceh.ac.uk  Thu Sep 17 11:37:24 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 17 Sep 2015 16:37:24 +0100
Subject: [Bio-Linux] Is anybody on this list using UGene on Bio-Linux?
Message-ID: <1442504244.32554.205.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

I've been doing a round of package updates this week and realised that
Bio-Linux ships with a very outdated version of the UGene workbench.  I
wondered if anyone is actually using it and if so do you:

1) Use the old version 1.9.8 that is installed by default
or
2) Get updates from the UGene PPA (as recommended on the UGene website)
or
3) Install updates for UGene via some other method?

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




From morais at iq.usp.br  Thu Sep 17 12:00:46 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Thu, 17 Sep 2015 13:00:46 -0300
Subject: [Bio-Linux] Is anybody on this list using UGene on Bio-Linux?
In-Reply-To: <1442504244.32554.205.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1442504244.32554.205.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CAAzi7naK+XRi69jSVmw-oNeUk0Ev+ZA9Y9JFkeb_=-VCPf-NVg@mail.gmail.com>

4) I did not know about UGene, but got interested.

On Thu, Sep 17, 2015 at 12:37 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> I've been doing a round of package updates this week and realised that
> Bio-Linux ships with a very outdated version of the UGene workbench.  I
> wondered if anyone is actually using it and if so do you:
>
> 1) Use the old version 1.9.8 that is installed by default
> or
> 2) Get updates from the UGene PPA (as recommended on the UGene website)
> or
> 3) Install updates for UGene via some other method?
>
> Cheers,
>
> TIM
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
> _______________________________________________
> 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 mashanovvlad at googlemail.com  Thu Sep 17 12:23:53 2015
From: mashanovvlad at googlemail.com (mashanovvlad)
Date: Thu, 17 Sep 2015 12:23:53 -0400
Subject: [Bio-Linux] Is anybody on this list using UGene on Bio-Linux?
In-Reply-To: <1442504244.32554.205.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1442504244.32554.205.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <55FAE919.60906@googlemail.com>

Ugene PPA

On 09/17/2015 11:37 AM, Tim Booth wrote:
> Hi,
>
> I've been doing a round of package updates this week and realised that
> Bio-Linux ships with a very outdated version of the UGene workbench.  I
> wondered if anyone is actually using it and if so do you:
>
> 1) Use the old version 1.9.8 that is installed by default
> or
> 2) Get updates from the UGene PPA (as recommended on the UGene website)
> or
> 3) Install updates for UGene via some other method?
>
> Cheers,
>
> TIM
>

-- 
--
Vladimir Mashanov, PhD
University of Puerto Rico
Ave Ponce de Leon / Ave Barbosa
JGD Building, Lab #220
Rio Piedras, PR 00931
phone: (787)7640000 x2596
email: mashanovvlad at googlemail.com
           vladimir at hpcf.upr.edu
Skype: vladimirmashanov
Twitter: @VMashanov
http://upr.academia.edu/VladimirMashanov



From xavier.depedro at vhir.org  Mon Sep 28 09:58:19 2015
From: xavier.depedro at vhir.org (Xavier de Pedro)
Date: Mon, 28 Sep 2015 15:58:19 +0200
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless VM on
	Ubuntu14.04?
Message-ID: <5609477B.3060202@vhir.org>

Hi:

This is my first message in this list, and let me start with a "thank
you" for such nice and useful project that "BioLinux" is.
Congratulations for the quality of the product achieved so far!

We are planning to use BioLinux for some hands-on work training sessions
for a Bioinformatics course we teach in a Masters Degree at University.
So far we have prepared a modified version of BioLinux8 virtual box
appliance (.ova) so that it includes the extra packages that we plan to
use in our course. So far, so good, for students with recent computers
(so that they can run the whole thing inside a virtualbox-powered
virtual machine in their computers).

But we are concerned expecting to have some students with old-ish
computers (from the 60 students enrolled in the course), and we did
setup another virtualbox-powered virtual machine with BioLinux8 on a
"Headless" server so that those students (5 or so?, we presume) will be
able to connect through RDP to one of our servers to use BioLinux there.
We followed these instructions for the setup:
https://www.howtoforge.com/vboxheadless-running-virtual-machines-with-virtualbox-4.3-on-a-headless-ubuntu-14.04-lts-server


However, only one RDP connection seems to be allowed at a time. I tried
these tweaks I could find around:

  "Ubuntu 14.04 ? Gnome Classic alike Desktop for XRDP : MATE-Desktop"
  http://c-nergy.be/blog/?p=5382
 
so that some new .xsession is created at the host for each new user
attempting to connect to the guest BioLinux8 through the host Ubuntu
14.04, but I didn't succeed... I presume the changes needed to have that
.xsession created for vboxheadless-version of the BioLinux are different
from the standard changes to have several RDP connections working
concurrently.

Any clue anyone?

Thanks in advanced!

Xavier



-- 
Xavier de Pedro Puente, Ph.D.
Statistics and Bioinformatics Unit (UEB) 
Vall d'Hebron Research Institute (VHIR)
Passeig de la Vall d'Hebron, 119-129
08035 Barcelona. Catalonia. Spain
 
Ph. +34 934894007 / Fax +34 934894015 
xavier.depedro at vhir.org
http://ueb.vhir.org

Collaborate: http://www.yoinvestigo.org - http://www.faigrecerca.org



From tony.travis at minke-informatics.co.uk  Tue Sep 29 06:23:31 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 29 Sep 2015 12:23:31 +0200
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless
 VM on Ubuntu14.04?
In-Reply-To: <5609477B.3060202@vhir.org>
References: <5609477B.3060202@vhir.org>
Message-ID: <560A66A3.5010301@minke-informatics.co.uk>

On 28/09/15 15:58, Xavier de Pedro wrote:
> [...]
> But we are concerned expecting to have some students with old-ish
> computers (from the 60 students enrolled in the course), and we did
> setup another virtualbox-powered virtual machine with BioLinux8 on a
> "Headless" server so that those students (5 or so?, we presume) will be
> able to connect through RDP to one of our servers to use BioLinux there.
> We followed these instructions for the setup:
> https://www.howtoforge.com/vboxheadless-running-virtual-machines-with-virtualbox-4.3-on-a-headless-ubuntu-14.04-lts-server
> 
> 
> However, only one RDP connection seems to be allowed at a time. I tried
> these tweaks I could find around:
> 
>   "Ubuntu 14.04 ? Gnome Classic alike Desktop for XRDP : MATE-Desktop"
>   http://c-nergy.be/blog/?p=5382

Hi, Xarvier.

Don't use RDP, use "x2go" - Bio-Linux 8 comes with the "x2go" server
pre-installed. You just need to install the "x2go" client on your
Windows/Mac desktop or laptop PC's. I'm particularly interested in
Bio-Linux as a terminal server, so please let me know how you get on?

The most important thing is to set the "x2go" client to use the MATE
desktop. I've used this to run Bio-Linux courses with 20 or more people
accessing the same server via "x2go" without any problems.

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


From xavier.depedro at vhir.org  Tue Sep 29 06:44:33 2015
From: xavier.depedro at vhir.org (Xavier de Pedro)
Date: Tue, 29 Sep 2015 12:44:33 +0200
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless
 VM on Ubuntu14.04?
In-Reply-To: <560A66A3.5010301@minke-informatics.co.uk>
References: <5609477B.3060202@vhir.org>
 <560A66A3.5010301@minke-informatics.co.uk>
Message-ID: <560A6B91.7010101@vhir.org>

He he, I presumed that this was going to be an answer. We are using
already X2Go in the production server (where we did start the virtualbox
machine with BioLinux), and I am still reluctant (feeling lazy and
conservative, maybe) to setup everything by hand there, since it might
interfere with other customizations we have in that production server
(and it took a while to have the whole thing working as intended; if
curious, ISPConfig3 setup with ssh-jailkit enabled in that server also).

I'm seriously considering that option, again (X2Go to url server and add
the biolinux repos, system upgrade, analyse the upgrade sh script for
biolinux I saw somewhere a few days ago, etc) , if I can't find another
less-risky solution (the RDP to a virtualbox-contained BioLinux server
seemed the safest approach for our case).

Thanks for the feedback already provided about this topic!

Xavier

El 29/09/15 a les 12:23, Tony Travis ha escrit:
> On 28/09/15 15:58, Xavier de Pedro wrote:
>> [...]
>> But we are concerned expecting to have some students with old-ish
>> computers (from the 60 students enrolled in the course), and we did
>> setup another virtualbox-powered virtual machine with BioLinux8 on a
>> "Headless" server so that those students (5 or so?, we presume) will be
>> able to connect through RDP to one of our servers to use BioLinux there.
>> We followed these instructions for the setup:
>> https://www.howtoforge.com/vboxheadless-running-virtual-machines-with-virtualbox-4.3-on-a-headless-ubuntu-14.04-lts-server
>>
>>
>> However, only one RDP connection seems to be allowed at a time. I tried
>> these tweaks I could find around:
>>
>>   "Ubuntu 14.04 ? Gnome Classic alike Desktop for XRDP : MATE-Desktop"
>>   http://c-nergy.be/blog/?p=5382
> Hi, Xarvier.
>
> Don't use RDP, use "x2go" - Bio-Linux 8 comes with the "x2go" server
> pre-installed. You just need to install the "x2go" client on your
> Windows/Mac desktop or laptop PC's. I'm particularly interested in
> Bio-Linux as a terminal server, so please let me know how you get on?
>
> The most important thing is to set the "x2go" client to use the MATE
> desktop. I've used this to run Bio-Linux courses with 20 or more people
> accessing the same server via "x2go" without any problems.
>
> HTH,
>
>   Tony.
>



From tony.travis at minke-informatics.co.uk  Tue Sep 29 08:50:18 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 29 Sep 2015 14:50:18 +0200
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless
 VM on Ubuntu14.04?
In-Reply-To: <560A6B91.7010101@vhir.org>
References: <5609477B.3060202@vhir.org>
 <560A66A3.5010301@minke-informatics.co.uk> <560A6B91.7010101@vhir.org>
Message-ID: <560A890A.10506@minke-informatics.co.uk>

On 29/09/15 12:44, Xavier de Pedro wrote:
> He he, I presumed that this was going to be an answer. We are using
> already X2Go in the production server (where we did start the virtualbox
> machine with BioLinux), and I am still reluctant (feeling lazy and
> conservative, maybe) to setup everything by hand there, since it might
> interfere with other customizations we have in that production server
> (and it took a while to have the whole thing working as intended; if
> curious, ISPConfig3 setup with ssh-jailkit enabled in that server also).
> 
> I'm seriously considering that option, again (X2Go to url server and add
> the biolinux repos, system upgrade, analyse the upgrade sh script for
> biolinux I saw somewhere a few days ago, etc) , if I can't find another
> less-risky solution (the RDP to a virtualbox-contained BioLinux server
> seemed the safest approach for our case).

Hi, Xavier.

If you can SSH into the VM, then you can use "x2go" to connect to it.

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


From morais at iq.usp.br  Wed Sep 30 16:31:11 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Wed, 30 Sep 2015 17:31:11 -0300
Subject: [Bio-Linux] r-cran-ape
Message-ID: <CAAzi7nYfcfESqcX85WaHepYvu9x4m0tghcd17+mR2T5WyaUYKQ@mail.gmail.com>

Hi,

   Any reason why package r-cran-ape is not present in trusty? It is on
precise.

Regards,
    Carlos
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