[JoanaTeixeira]

Yes, you are right.
I fixed my mistake but something isn´t OK:

Joana Teixeira@Joana /c/curl/samples
$ ruby -e "$(curl -k https://raw.githubusercontent.com/Ho...nstall/master/
install)"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 7859 100 7859 0 0 9678 0 --:--:-- --:--:-- --:--:-- 9678

Joana Teixeira@Joana /c/curl/samples
$ brew install bedtools
sh: brew: command not found

[GenoMax]

$ brew install bedtools
sh: brew: command not found

Try (if brew file is in current directory then omit the /path_to/ part).

$ /path_to/brew install bedtools

If that does not work then

$ chmod u+x /path_to/brew
$ /path_to/brew install bedtools

[JoanaTeixeira]

I searched for brew on my computer and I don't found.
I think that installation is failing and I don’t know why.

[GenoMax]

I think you have compiled other software yourself so why not do "bedtools" the same way. Get the source code and compile it. Do not worry about brew.

[JoanaTeixeira]

I tried to do this, but it didn't work.

I followed these steps:

(http://bedtools.readthedocs.org/en/l...llation.html)- Compiling from source via Google Code.

[JoanaTeixeira]

Joana Teixeira@Joana /c/bedtools
$ curl http://bedtools.googlecode.com/files....2.23.0.tar.gz > BEDTools.t
ar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1453 100 1453 0 0 4429 0 --:--:-- --:--:-- --:--:-- 4429

Joana Teixeira@Joana /c/bedtools
$ tar -zxvf BEDTools.tar.gz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

[GenoMax]

Joana Teixeira@Joana /c/bedtools
$ curl http://bedtools.googlecode.com/files....2.23.0.tar.gz > BEDTools.t
ar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1453 100 1453 0 0 4429 0 --:--:-- --:--:-- --:--:-- 4429

Joana Teixeira@Joana /c/bedtools
$ tar -zxvf BEDTools.tar.gz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

See if you can use gunzip to extract followed by tar.