[qnc]

Thanks guys having a bit of a mental block here..

Am I suposed to:

Create the following folders inside my BEDTools-v2.13.3/bin folder:
/usr/local/bin/

and then place whole folders with *.cpp , *.h and Makefiles into that?

Will the commands work when I type then then?

[GenoMax]

Noooooooooo

Change to the directory where you have the BED files you want to manipulate with BEDTools.

Then use the full path to your BEDTools executables (/path_to/BEDTools-v2.13.3/bin) as I had shown in the example in my previous post (#12 in this thread).

See this link for explanation of UNIX filesystem paths: http://ultra.pr.erau.edu/~jaffem/tut...tem_basics.htm

Thanks guys having a bit of a mental block here..

Am I suposed to:

Create the following folders inside my BEDTools-v2.13.3/bin folder:
/usr/local/bin/

and then place whole folders with *.cpp , *.h and Makefiles into that?

Will the commands work when I type then then?

[qnc]

That BEDTools-v2.13.3/bin is empty on my system does that mean it wasn't unpacked/complied properly?

[qnc]

I don't think /usr/local/bin exists under OSX by default, so you may have to create it (e.g. "sudo mkdir -p /usr/local/bin") or copy the files to a different directory in your PATH. You didn't destroy anything when you forgot the cp command, you just confused sudo. BTW, you may want to ensure that /usr/local/bin is actually in your PATH (type "echo $PATH" and see if it's listed), otherwise make sure to add it.

DO I create this in the BEDTools folder?

i.e. cd to BEDTool then "sudo mkdir -p /usr/local/bin"

And then its an empty folder do I have to put something in it?

Sorry will get this eventually

[GenoMax]

Can you look in the "src" directory to see if the files remain there? It is possible that compiled files were not moved to the "bin" directory.

That BEDTools-v2.13.3/bin is empty on my system does that mean it wasn't unpacked/complied properly?

[qnc]

Thanks for helping me trouble shoot this guys I really do appreciate this.

GenoMax I am using:

Mac OSX 10.6.8
Terminal version 2.1.2 (273.1)

I used the commands as they gave in
BEDTools-User-Manual.v4.pdf page 17


$ curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz $ tar -zxvf BEDTools.tar.gz
$ cd BEDTools
$ make clean
$ make all
$ sudo cp bin/* /usr/local/bin/

Should I run it again and see if there are any error message which might help get to the bottom of this?

[qnc]

Here is what the src folder looks like

[dpryan]

I can confirm that the standard Makefile copies things properly to the bin/ directory on OSX (just tried it on the laptop).
This is the directory containing the actual compiled programs (the *.cpp and *.h files are source code):


You can either copy those somewhere or just execute them where they are (either will work). If running through the commands provided in your most recent post (well, the one prior to the post with the image) doesn't produce an error message then things should be installed and ready to use. BTW, if you happen to have a friend/colleague nearby that's familiar with Linux then he/she should be able to help you as well.

[qnc]

Ok will retry the complie and let you know.

If I get any errors I'll post them up here.

[qnc]

Ok it seems to have worked... but is still not working?

here is the bin now with the programs and two small bed files (less.bed & more.bed) just to see if it is working but I get the following return on the command. I have cd to the bin folder and can see the files/programs with a ls command

$ intersectBed -a less.bed -b more.bed
-bash: intersectBed: command not found



What is going wrong!!

[GenoMax]

Issue the command like this:

$./intersectBed -a ./less.bed -b ./more.bed

You need to tell the shell to look for the program in the current directory.

Ok it seems to have worked... but is still not working?

here is the bin now with the programs and two small bed files (less.bed & more.bed) just to see if it is working but I get the following return on the command. I have cd to the bin folder and can see the files/programs with a ls command

$ intersectBed -a less.bed -b more.bed
-bash: intersectBed: command not found



What is going wrong!!

[qnc]

Awesome!!!


$ ./intersectBed -a less.bed -b more.bed
chr6 112879106 112879267 D6S474 1000 + 112879106 1chr69267119553773,0,0, 119553939 D6S287-L-5-18 1000 + 11955377chr6 124656623 124656633 SNP_A-1677306 1000 + 124656628 124656628 255,0,0

We have lift off.

Thanks guys... amazing got there in the end and I learned a lot thank you.

No doubt I'll have more questions but for now...

Thank you!

[GenoMax]

Excellent