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Old 12-01-2015, 11:40 PM   #1
gsgs
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Default bio-knoppix bioknoppix

I just found this:

http://bioknoppix.hpcf.upr.edu/


alas, the last update was from 2008

is there a more actual similar project ?

-------------------edit 2015/12/10-------------------
http://bioknoppix.hpcf.upr.edu/downloads
bioknoppix is 688MB for download as an "iso" file
but none of the 5 mirror sites were available

> For those who have slow internet connections you can buy a bioknoppix-0.2.1beta cd for a
> nominal fee at http://cheapbytes.com. It is also available at http://linuxcd.org.

none of these links work for me

http://www.bicpu.edu.in/biotools.htm
> Bioknoppix is a customized distribution of Knoppix Linux Live CD. With this distribution you
> just boot from the CD and you have a fully functional Linux OS distribution with open source
> applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn't
> touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc.

the Spanish mirror may have changed to ftp://ftp.rediris.es/mirror/
but I didn't find it there either

Last edited by gsgs; 12-10-2015 at 06:19 AM.
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Old 12-02-2015, 02:00 AM   #2
GenoMax
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There is: http://environmentalomics.org/bio-linux/

You may also find it easier to run ubuntu or other unix distro in virtual box on Windows. That said make sure you have beefy enough hardware available. STAR will require lots of RAM no matter where it runs (in virtual box/or natively).
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Old 12-02-2015, 06:16 AM   #3
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I can just buy a new notebook with lots of RAM and Linux (will the knoppix - USB - stick work ?)
No problem.
(can't we use micro-SDs as RAM ? or is it too slow)

But how long will it take me to get familiar enough with Linux ?

And then, I still have to export everything back to Windows-cmd.exe=DOS,
since I have all my utilities there

maybe I should have switched to Linux long ago
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Old 12-02-2015, 01:04 PM   #4
GenoMax
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No you can't use SD cards as a replacement for RAM. They are probably too slow to be used for computation also.

If you are reasonably computer savvy you could bring yourself up to speed on unix in less than a week. I will include this link in case you feel inclined to do this.

What sort of utilities do you have/need on windows side? We can perhaps suggest unix equivalents so you could just stay in the unix world.
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Old 12-02-2015, 10:49 PM   #5
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ahh, I spent another 3h this morning to get Linux running on my other notenook to no avail.
I have 2 knoppix USB-sticks, and ~5 DVDs to boot from but all that I could get was freedos,
and then, later, when I gave up, even that didn't work.The originally installed Windows is also
no longer available and it takes so long to boot and wait until I decide that there is no progress.
Or long tedious licences ("openSuse") which I won't read.
And sorting cables ...

It has 3.6GB RAM and 2 CPUs with 2.4GHz each.
I got 20 Computers running simultaneously without keyboard,monitor, HDs, and shared RAMs
and floppies, but that was 15y ago and I'm probably no longer "computer savvy")

Also, "in a week" is much time for a software that costs nothing and what I don't even know yet
whether it will work for me.

My software is mostly self-written over the years, adapted to my needs,
so there is no good replacement.

----------edit--------------
I ordered "Linux Fedora 23" USB-stick now from the UK, let's see ...
And also "Ubuntu" DVD, since someone mentioned Ubuntu here.
And also 4 more Knoppix "bootable" DVDs, several versions.

Last edited by gsgs; 12-02-2015 at 11:09 PM.
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Old 12-03-2015, 05:39 AM   #6
sklages
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What are you expecting?
What are your plans with "biolinux"? What are you trying to achieve?

Didn't get it ..
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Old 12-03-2015, 05:51 AM   #7
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one thing that recently became more and more necessary is fast alignment
of large datasets. This occurred in another thread here : the "Star" software
was available only for Linux.
But it's a general problem, almost all the Universities only use Linux/UNIX,
so the research software is often not available in Windows.
It's particularly true for the field of interest here, which is Bioinformatics.
Bio-Knoppix could be viewed as an attempt to make this available to
Windows Users - the large majority in non-Education-life


So, I want to be able to compile,run,download,edit,convert .... the Linux software
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Old 12-03-2015, 06:05 AM   #8
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@gsgs: If you want to stay in windows you could use BBMap, which is a great NGS data suite (multiple tools, more info in this thread: http://seqanswers.com/forums/showthread.php?t=58221). It is written in java so will run on windows without need for any changes.

BTW: 3.6 G of RAM is not going to take you far with pretty much any software that is related to NGS. STAR requires ~30GB of RAM for mapping to the human genome (could be reduced to 16GB in the "sparse" mode with some speed loss). Not sure what kind of data you are going to be working with.

A "week" was a very rough estimate of how long it would take to gather the basics of unix. It sounds like you certainly know your way about hardware/software, so it may take you a day or less. Just depends on how serious you are going to be about making the switch. You don't need to let go of windows. Many of us do use windows on our primary desktops. Just add linux to your repertoire. It will serve you well over time.
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Old 12-03-2015, 06:08 AM   #9
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So there is some need for you to get linux running. If you want to compile, run, download etc. "bioinformatics" software you should at least understand the basics of a linux system.
So "in a week is much time for a software that costs nothing and what I don't even know yet whether it will work for me" makes no sense IMHO when you want to efficently use such software.

As already mentioned by GenoMax, trying to start with Ubuntu/Mint is not a bad option.
If you have problems installings such linux on your device(s), you should probably post your issues on the approbiate forums. As a (german) starting point for Ubuntu you might want to check e.g. https://wiki.ubuntuusers.de/Einsteiger ..
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Old 12-10-2015, 03:55 AM   #10
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ok, I spent another 2h to figure out linux ...
The knoppix actually did boot before just that I didn't realize it had finished booting.
I had interpreted the screen as some "booting art".
Some other CDs or one usb-stick didn't boot, though. Displaying errors about CPU or missing "grab.exe"
I also could boot "fedora". Booting from usb=stick takes ~70s, booting from CD/DVD takes ~160s.
You have to press F12 permanently on switching on to enter the boot-menu and then
choose USB or CD/DVD respectively, but wait 30s for CD/DVD, until there are no more
CD-read-noises, before you press enter. Took me a while to figure that out.
Then in knoppix choose the screen-symbol on the bottom bar to enter "bash" commandline-mode,
and then use the linux equivalents for DOS/Windows , e.g. "ls" for "dir" etc.
There are probably lists on the internet for all the commands.
However, there doesn't seem to be a C++ compiler included in knoppix or fedora ?!
So, which compiler will compile star under knoppix-linux or fedora-linux or what linux and what
compiler do I need ?

I still think in such cases a whole computer with the software installed should be sold.
Or at least a booting micro-sd card or usb-stick, that runs the software automatically from
batch and writes the result back to the sd-card.
Aligning the sequences in a file with default name.

I would be interested to read other Windows-->Linux switchers' experiences with bio-(linux)-software
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Old 12-10-2015, 04:11 AM   #11
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thanks for the replies above. (I didn't get an email about that, as usual)
GenoMax,
I don't know about Java. Also, I can't entirely switch to Linux, I still need my DOS/Windows tools,
so I have to use both. Why is 3.6 GB not enough for human DNA ,
you do one chromosome after the other ?! Or 10000 flu sequences with 2000 nucleotides each
And why can't it use SD-card or HD as RAM, even if it is slower ?
I do feel that it's the algo that gives much more improvement (over MAFFT) than the hardware

For Linux ... in commandline modus it should be almost the same as DOS. I wouldn'r be surprised
if there is an easy tool that converts DOS-commands to the corresponding Linux commands ?!
---------------------------------------------------
sklages,
I just feel that it is not well designed for "Einsteiger" , there should be an "easy-mode", foolproof
just for the basics. On the first home computers the operating system was installed on ROM,
the programming language or compiler was just one executable.
Then came more features and options ... but also more compatibility problems, more errors,
more complicated and longer manuals. "More" is not necessarily an advantage.
I gave up German forums, English traffic is usually ~10 times more
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Old 12-10-2015, 04:23 AM   #12
sklages
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Your issue is pretty off-topic here. You should get familiar with some basic linux stuff, as I wrote.

http://lmgtfy.com/?q=linux+c%2B%2B+compiler

I still don't get what you are trying to achieve ..
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Old 12-10-2015, 04:26 AM   #13
gsgs
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I can't be the only one with such problems ?!
IMO it's of basic importance for using bio-software.

I'm trying to get the whole process easier, including compiling,
compatibility ,

Last edited by gsgs; 12-10-2015 at 04:29 AM.
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Old 12-10-2015, 04:31 AM   #14
sklages
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Quote:
Originally Posted by gsgs View Post
thanks for the replies above. (I didn't get an email about that, as usual)
sklages,
I just feel that it is not well designed for "Einsteiger" , there should be an "easy-mode", foolproof
just for the basics. On the first home computers the operating system was installed on ROM,
the programming language or compiler was just one executable.
Then came more features and options ... but also more compatibility problems, more errors,
more complicated and longer manuals. "More" is not necessarily an advantage.
I gave up German forums, English traffic is usually ~10 times more
The "easy-mode" is called "Desktop Envionment". The power of linux/unix is not the "easy-mode" but the command line and the large number of tools. You are not urged to use the command line to use linux and some bioinformatics software. But you won't get far without command line...

my 2p ;-)
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Old 12-10-2015, 04:42 AM   #15
gsgs
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command line would be ok for me, I'm using it in DOS (windows-cmd)
I'm not sure whether that desktop environment is usually easier and should be recommended
for bio-software. But I'm a Linux,beginner, what do I know ...
In DOS however I found it superior in such tasks, where you handle and manipulate shared files and use multiple
software.

--------------edit-----------------

What's the Linux equivalent to Windows batch files?

someone replied:
> You need to learn to write bash scripts. These are the Linux equivalent of
> windows batch files. The syntax isn't too difficult to get your head around.
> I suggest googling as there are many great freely accessible tutorials.

another reply:
> Make sure you have installed wine , then do the following command in a terminal:
> wine cmd
> This will open up a Windows command prompt. Start your .bat from there.
[sounds good to me, searching wine ...https://en.wikipedia.org/wiki/Wine_(software) :
> aims to allow applications designed for Microsoft Windows to run on Unix-like
> operating systems.
> ... Wine does not have good support for MS-DOS, but starting with development
> version 1.3.12, Wine tries running MS-DOS programs in DOSBox if DOSBox is
> available on the system.[48] However, due to a bug, current versions of Wine
> incorrectly identify Windows 1.x and Windows 2.x programs as MS-DOS
> programs, attempting to run them in DOSBox (which does not work).[49]



another reply:
> You might want to learn python.
> It's easy to learn and more readable than some other scripting language... ;-)

[sound really complicated to me]

----------------edit-----------
seems that "wine" is included in knoppix since version ~7.0.3

Last edited by gsgs; 12-10-2015 at 05:03 AM.
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Old 12-10-2015, 08:39 AM   #16
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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.
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Old 12-10-2015, 11:43 AM   #17
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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
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Old 12-10-2015, 12:23 PM   #18
GenoMax
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Quote:
Originally Posted by gsgs View Post

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

Code:
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
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Old 12-10-2015, 09:15 PM   #19
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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
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Old 12-12-2015, 12:44 AM   #20
gsgs
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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...-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/v...p?f=63&t=52566

Last edited by gsgs; 12-13-2015 at 10:26 AM.
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