install bedtools in mac os x

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khaled alqahtani

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Oct 6, 2013, 9:36:42 AM10/6/13
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i tried to installed betools in my mac but i do not know what is going wrong
i looked in Google and i found that i have to download Xcode. i already downloaded it .

curl http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz > BEDTools.tar.gz
tar -zxvf BEDTools.tar.gz
cd /Users/joojoo210/Desktop/bedtools-2.17.0
make

the error is :
make: command not found
 Also i read one articale which suggest to try Homebrew, which still includes the installation
of Xcode, installing BEDTools would be as easy as:
$ brew install bedtools
but there was an error saying :
Error: No available formula for bedtools
now i have spent 3 days just looking to install bedtools to Convert the (filtered) bam files to bed files, using bedtools :

setup bedtools
bamToBed -i LS.bam > LS.bed.

any help will be appreciated

Aaron Quinlan

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Oct 7, 2013, 8:10:20 AM10/7/13
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I am unsure about HomeBrew, but the make error you are getting suggest you did not properly install the "command line tools" with Xcode. 

This article may be helpful:

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Arjan

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Dec 4, 2013, 11:15:18 PM12/4/13
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Another option is to use macports. Bedtools has recently been added to macports.

Regards,

Arjan
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