Cloud Bio-Linux developments

[Tim]

Hi All,

Just to kick off the new discussion forum here, I'd like to put a
record of some of the recent discussions and happenings that have been
going on regarding CBL. Ntino gave an excellent talk (slides:http://
gensc.org/gc_wiki/images/2/29/GSC11-Ntino-Krampis.pdf) at the recent
Genomic Standards Consortium (GSC) meeting in Cambridge, UK and we met
in person to discuss how we could make progress on developing and
promoting Cloud BioLinux.

Bio-Linux on the cloud now has a published mention (albeit a passing
one) thanks to the BOSC proceedings paper "Galaxy CloudMan: delivering
cloud compute clusters, Afgan et. al" which Brad co-authored.

We're working on a proper Cloud BioLinux publication and Brad has put
a lot off effort in the last few days to enable the
"cloudbiolinux.org" site and tidy up the code hosting and discussion
list.

I've been working on adding packages to Bio-Linux and especially in
contributing my packaging efforts to the Debian-Med package
repository. As these go through the system they will be available to
all Debian/Ubuntu users but before that they will be added to the CBL
build in the near future.

TIM

[Rodrigo Barban Zucoloto]

Hi,

Could someone help me? I have an 32 bits ubuntu 14.10 installed at my laptop and decide training Bioinformatic following Bl8 lastest introduction (http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf).

So, after adding the lines to my sources.list

deb http://distro.ibiblio.org/bio-linux/packages/ unstable bio-linux
deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main

I could install the major 64 bits bio-linux packages but some of them could not be installed (File attached).

How could I get the lost packages to satisfy this dependencies?

I saw that base directories are how unsupported at 64 bit version of biolinux, but is in the list of packages of Cloud-Biolinux. I wish to know here can I get this lost packages!

Thank you,

Rodrigo Barban Zucoloto.

[Tim Booth]

Hi Rodrigo,

You say you have a 32-bit system. Many newer bioinformatics packages
need 64-bit. For example, the actual QIIME package is here:

http://distro.ibiblio.org/bio-linux/packages/dists/unstable/bio-linux/binary-amd64/bio-linux-qiime_2:1bl-10_amd64.deb

The one that was failing to install was an old version that was still on
the server, but even that relied on 64-bit packages to run.

Also most of the packages you listed are either deprecated or useless to
you. The CloudBiolinux package list is out of date. The only one you
would actually want is dialign, in which case just "apt-get install
dialign". That will work on 32-bit.

Cheers,

TIM

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--
Tim Booth <tbo...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre

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

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

[Tony Travis]

On 26/03/15 20:27, Rodrigo Barban Zucoloto wrote:
> Hi,
>
> Could someone help me? I have an 32 bits ubuntu 14.10 installed at my
> laptop and decide training Bioinformatic following Bl8 lastest
> introduction
> (http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf).
>
> So, after adding the lines to my sources.list
>
> deb http://distro.ibiblio.org/bio-linux/packages/ unstable bio-linux
> deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
>
> I could install the major 64 bits bio-linux packages but some of them
> could not be installed (File attached).
>
> How could I get the lost packages to satisfy this dependencies?
>
> I saw that base directories are how unsupported at 64 bit version of
> biolinux, but is in the list of packages of Cloud-Biolinux. I wish to
> know here can I get this lost packages!
>

Hi, Rodrigo.

My advice is first find out if you have a 64-bit CPU in your laptop. For
example, on my laptop "beluga":

ajt@beluga:~$ fgrep name /proc/cpuinfo
model name : Intel(R) Core(TM) i5-2450M CPU @ 2.50GHz
model name : Intel(R) Core(TM) i5-2450M CPU @ 2.50GHz
model name : Intel(R) Core(TM) i5-2450M CPU @ 2.50GHz
model name : Intel(R) Core(TM) i5-2450M CPU @ 2.50GHz

If you do have a 64-bit CPU, then install Bio-Linux 8 (based on 64-bit
Ubuntu 14.04 LTS) on your laptop instead of trying to adapt your
existing 32-bit Ubuntu 14.10. However, if you only have a 32-bit CPU in
your laptop, it might be better to run CBL (Cloud-Bio-Linux) on AWS and
use your laptop as a terminal instead. You will need to install
"x2goclient" on your Ubuntu 14.10 laptop in order to use CBL with a
remote MATE desktop GUI on AWS:

apt-get install x2goclient

HTH,

Tony.