[GenoMax]

You are running 32-bit version of ubuntu (http://cynwong.com/blog/?p=15).

I suggest you add the flag that Heng Li (author of BWA) had suggested in the link I had posted in #4 above and see if that works. You will have to edit the Makefile in the source code you downloaded.

[Superbug]

Ok

As you probably might have guessed already, I am a NEWBY
So the flag he suggested is "gcc -msse2" (?!) or is this what I have to change in the source code ?!

The Makefile has in its firs row "gcc".

[GenoMax]

Add it to the CFLAGS line in the Makefile.

CFLAGS= -msse2 -g -Wall -Wno-unused-function -O2

[Superbug]

Thanks a lot!

I did everything you said, and the make command also worked now.

Just when I now check which version I have, it still says 0.7.5a-r405, even after a re-start.....

These problems never end.....

[GenoMax]

That is because you have the bwa that came with the VM in your $PATH. If you explicitly run the newly compiled bwa by providing full path to the executable it should work.

$ /full_path_to_new/bwa

You are almost there.

[Superbug]

I honestly have no idea what you just "said"

I do understand that I have to tell my VM now that it should use the new bwa.
But where and how with the command you have written, I have no idea.....

[GenoMax]

Go to the directory which has the new bwa in it.

$ pwd

That should give you the path to that directory. Now you can run the new bwa while you are still in that directory

$ ./bwa

Or if you go to some other directory then you can still refer to the new bwa by using the full path like this:

$ output_you_got_from_pwd_command_above(replace the real value here)/bwa

[Superbug]

Oh jeezz...
So I got the directory where the bwa is in, which is /home/wt/BWA/bwa-0.7.9a/bwa

But when I use this pathway to run the actual command I only get error messages that such a file or directory can not be found....

The commands I need to run are bwa aln or bwa sampe!

So what I did now, is copy paste the "bwa" file out of this folder into the path where my files are that I need to run.... Will that work ?!

[Brian Bushnell]

The latest bwa (0.7.x) does not support aln and sampe, just bwa mem (which is better, anyway). If you want to do bwa aln you need an older version, like 0.6.x or 0.5.x.

[Superbug]

That can not be true, as I currently have 0.7.5a and run the aln and sampe commands.
And I can also see them when I type "bwa".

[GenoMax]

You have to make sure that the new bwa is executable

$ chmod u+x /home/wt/BWA/bwa-0.7.9a/bwa

Then if you run

$ /home/wt/BWA/bwa-0.7.9a/bwa

it should print the help for bwa out.

aln is still available with 0.7.9.

[Superbug]

That is good to know - about being executable.
The alignment is running..... Exciting.... Let's see how far it gets this time....

Thanks already for all your help !!!!

[GenoMax]

So what I did now, is copy paste the "bwa" file out of this folder into the path where my files are that I need to run.... Will that work ?!

No you do not need to do that. Just include the full path to the new bwa executable when you run your alignment commands in the new directory.

Unix commands can use "relative" paths (it would help to go through this tutorial: http://korflab.ucdavis.edu/Unix_and_...1.1.html#part1) and can be used in any logical combination from anywhere on locally available filesystems.

[Brian Bushnell]

That can not be true, as I currently have 0.7.5a and run the aln and sampe commands.
And I can also see them when I type "bwa".

The latest releases do not support them at all, but aln has been broken or unstable in most of 0.7.x, so if you want to use it, you will be better off with 0.6.x. At least, that was the case last time I checked.

[Superbug]

That copy past action was something I came up before knowing that I need to do bwa executable

So now I run it the way you said.....

Will have a look at the tutorial, thanks !!!!

Thanks again !!!!!