Re: debian science biology live usb? or biolinux
Hi Ibrahim,
you probably want to contact rather debian-medibrahim@lists.debian.org
than this mailing list which is rather about technical things - so I
changed the list address in CC.
On Mon, Sep 26, 2011 at 07:50:39AM -0700, ibrahim acikbas wrote:
> Hello Mr Tille,
> I am moleculer geneticist.
> I am not familiar unix and linux OSs or any complilation and programing.
> Unfortuanetly our institution do not have a bioinformatic facility.
> I used to be some DOS commands. I have installed ms-winXP+bsd on same harddisk in pentium4 machine a few years ago but I used rarely and I could not be use effectively.
>
> I need unix/linux OS for several genetic programs work on as well as emboss tool. I can not dedicate a separate PC for this now. I am planning to set up a live usb and use it on a ms-win xp pro sp3 pc machine:
> gigabyte G31M-SL2 mainboard,
> Pentium dual core E5200 3.38Ghz (32bit),
> 3GB RAM,
> Nvidia GeForce 9500GT video-card with own 1GB memory.
> one samsung 120GB harddisk with two partition.
> (usb mouse/keyboard, usb laser printer samsung ML1610, Hans-G 19" squre LCD monitor with vga connection, 1280x1024 on winxp)
>
> Some linux based bio-genetic programs Biolinux 5 (32bit), Debian scientific Biolgy blend, DNAlinux, Bioslax, Scientific linux, bioknoppix...are based on debian and/or ubuntu. This linux program may be more easeir for non familiar end users as me. However I were found desktopBSD in net. I hope the programs Phase, Haplotyper etc work on desktopbsd, but don't have any ideas in linux.
I guess if you are a bit comfortable with some BSD version (which I do
not know) you will not experience problems with a usual Debian
installation.
> I think to try some live unix/bsd versions (because I want to write my data, input, output, sample... files on the same usb) but generally not recommended to me, they rather suggest ubuntu is an easier starting, I think because of my unfamiliarity. After I was read about desktopbsd, I am be sure of myself. Please excuse me about that I asked a bsd question to a debian expert.
>
> In biolinux and debian science bio I think all biosoftwares is installed as well as os and etc, ready to use.
> However If I chose bsd way, the easy part is only desktopbsd, I think I will do everything myself and not easy for me: software downloads and installing these to bsd, may be organizing some make files.
>
> What your suggesion to mine condition?
I can not tell if this is the best solution for you but if you want to
test Debian Med you just need to fetch a usual Debian install image from
www.debian.org and once you have installed it you install med-bio (either
via the graphical installer or you can also say
sudo apt-get install med-bio
on the command line.
> Where and how can I download any stable debian science bio live usb (blend) image?
Currently no such thing like a ready to install image because in
principle the way described above is easy enough (but we are considering
it for the future anywy).
> Can I download, prepare and install the image on usbstick in a ms-winxp machine? I have not any linux pc.
There is advise on www.debian.org how to do this.
> Can I make partitions in live usb? should I do?
I can not answer this simply because I do not know whether you want to
have a dual boot machine. If not the installer gives reasonable advise
how to partition your computer.
> How do I install /use my boiscientific programs don't already installed in debian, like phase, unphased, haploview, famhap, tomcat ?
Please discuss this once you are finished with your box. Just ask what
program you are missing and we try to help you step by step.
> Can live usb see my winxp partitions (C: and D: FAT/NTFS)? and make file transfer? may be from a swap area?
If you have a dual boot machine the Win particions can be accessed from
Linux. I have no experience with this (I was never running any Windows
machine, but as far as I know FAT is the easier solution if you want to
access it from Linux. I have heard that recently NTFS can be used with
read+Write access - but I can nut guarantee this.
> Phase: http://stephenslab.uchicago.edu/software.html
> Unphased: http://www.mrc-bsu.cam.ac.uk/personal/frank/software/unphased/
> Haploblock: http://www.cs.technion.ac.il/people/dang/
> Haploview: http://www.broad.mit.edu/personal/jcbarret/haploview/
> Tomcat: http://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html
> SNPhap: http://www-gene.cimr.cam.ac.uk/clayton/software/
> Famhap: http://www.uni-bonn.de/~umt70e/becker.html
I admit that those programs do not sound familiar (except for haploview
where we did some preparations) but we are there to care for packages
our users are interested in. CUrrently I'm on vaccation but once I'm
back I might add those programms to our todo list and we will try to
work down your list. Remark: Tomcat is a quite bad name for such a
program considering that there is a quite famous other program with thsi
name (apache application server).
Kind regards and thanks for your interest in Debian Med
Andreas.
--
http://fam-tille.de
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