[GenoMax]

I suspect that some of the boot problems you are having may be because of hardware that is dated (what specs does your laptop have and how old is it)? Starting with some recent hardware will simplify things. You could put together a cheap build yourself (not sure about german pricing) perhaps for around 200 euro that would allow you to avoid many of these boot issues.

GNU C compile (gcc) is what you want. If fedora or other unix does not come with it you can find installation instructions for the distribution.

In terms of a "ready to run" solution I would have thought that "biolinux" would fit the bill.

[gsgs]

that was a Dell ......Alternate... or such, bought some years ago. , Windows was on it,
but no longer runs. Afterwards you always know better ...
Ok, bio-linux sounds good. Maybe it's even the reason why bioknoppix is discontinued
I'm downloading overnight ... I hope that works. 1.7GB already, I don't know how much it will be in total.
I can't use files >4GB on this old computer.
I also like the idea of "wine" or "Zorin" or BBMap, so to use Windows/DOS programs in Linux
I had used gcc before in Windows and could compile some Unix programs 10 years ago.
Maybe a windows update would also work. I remember, I had problems with
the "makefile". I may also have used Cygwin successfully for the MAFFT-aligner, I forgot.

------------------------------------------

Zorin OS is an Ubuntu-based Linux distribution designed especially for newcomers to Linux. It has a Windows-like graphical user interface and many programs similar to those found in Windows. Zorin OS also comes with an application that lets users run many Windows programs. The distribution's ultimate goal is to provide a Linux alternative to Windows and let Windows users enjoy all the features of Linux without complications.


I failed with bbmap. First they tricked me into downloading another file, but I won't read their
7zip "gorilla" terms.... Then I succeeded to get a 4MB gzip file.
gzip -d , ren as ".tar" , but extar converts to DOS-names and lots (hundreds ?) of rename requests.
773 files, but no .exe

[GenoMax]

I failed with bbmap. First they tricked me into downloading another file, but I won't read their
7zip "gorilla" terms.... Then I succeeded to get a 4MB gzip file.
gzip -d , ren as ".tar" , but extar converts to DOS-names and lots (hundreds ?) of rename requests.
773 files, but no .exe

You may not have other choice but to use 7-zip if you want to work with tar/gzip files on Windows. There are no exe files since Brian's programs is written in java. You will need to have Java (1.7/1.8) installed on windows and will run eventually run like this

Windows prompt> java -Xmx23g -cp /path/to/current align2.BBMap in=reads.fq out=mapped.sam

@Brian has examples here for all his programs: http://seqanswers.com/forums/showthread.php?t=41057

[gsgs]

the first download of bio-linux failed, I have no resulting file.
The 2nd download produced a file of exactly 2^31=2147483316 bytes
so I wonder whether that is some error with my system or browser or provider,
not allowing/interrupting such big downloads. (I never did it before, afair)

as for BBmap, it looks too complicated, too many files, and I don't know Java
and that thread is so long and I don't know your bio-terminology

Maybe I should wait that some of the assembly gurus writes an aligner in <1000 bytes ...
I do remember those old competitions

[gsgs]

http://www.biomedcentral.com/1471-2105/14/243

We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux
...
central GNU/Linux server on the campus and allow students to connect by Secure Shell, ssh
(‘the server approach’). The server will typically run either a standard
Linux distribution or a
specialist bioinformatics distribution such as NEBC Bio-Linux [4].
...
specialist bioinformatics distribution such as DNA Linux Virtual Desktop Edition [5]
(‘the VM approach’).
...
Linux system on removable media (‘the USB stick approach’, for example [6];
...
buy laptops of a specific kind, with a suitable operating system, data and software installed
(‘the laptop approach’) This avoids hardware incompatibilities that the
USB stick approach may, in practice, experience [6].

loaning a Raspberry Pi computer [8] and associated peripherals to students for the duration
of the course (‘the Raspberry Pi approach’).
...
The Raspberry Pi is more than adequate for the task.
...
and a wide range of bioinformatics packages [19].
The latest version, including Linux, software and BLAST databases,
is available at the 4273π Web site [25].

http://eggg.st-andrews.ac.uk/4273pi

Licence:4273πBioinformatics for Biologists has a Creative Commons Attribution licence (http://creativecommons.org/licenses/by/2.0 webcite)

------------------------------------------------------

4.Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M:
Open software for biologists: from famine to feast.
Nat Biotechnol 2006, 24:801-803. PubMed Abstract | Publisher Full Text
5.Bassi S, Gonzalez VC: DNALinux virtual desktop edition.
Nature Precedings 2007.
http://dx.doi.org/10.1038/npre.2007.670.1
6. Bio-Linux 7 USB memory sticks.

http://nebc.nerc.ac.uk/tools/bio-linux/live-usbkey

[the webpage has changed, I can't find the stick on the new webpage]
8.Raspberry Pi: An ARM GNU/Linux box for $25.
http://www.raspberrypi.org webcite
19.Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K,
Goble C, Holland R, Belhachemi D, Plessy C: Community-driven computational
biology with Debian Linux.
25.4273π.

http://eggg.st-andrews.ac.uk/4273pi

http://www.biomedcentral.com/content/supplementary/1471-2105-14-243-s2.zip

zip of 7.3MB , the course
21 files : 15 pdf, 3 .fa , 3.txt , 8.8MB decompressed


==================================================

but it's 6.5 GB and 30GB uncompressed ! :-(

https://www.raspberrypi.org/forums/viewtopic.php?f=63&t=52566