how to install BedTools in a user directory

[alittleboy]

I am trying to install Bedtools in a user directory, however I looked at the manual for its makefile, and there is no such argument like "--prefix" for me to change. Is there a way to install all Bedtools in a directory that I specify? Thanks! I am under the Linux system.

[dariober]

I am trying to install Bedtools in a user directory, however I looked at the manual for its makefile, and there is no such argument like "--prefix" for me to change. Is there a way to install all Bedtools in a directory that I specify? Thanks! I am under the Linux system.

After executing "make" you should have a bin directory with the compiled executables. Just copy the executables to your favaourite directory and you are done. This is from the docs http://bedtools.readthedocs.org/en/l...tallation.html

$ curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
$ tar -zxvf BEDTools.tar.gz
$ cd BEDTools-<version>
$ make

At this point, one should copy the binaries in ./bin/ to either usr/local/bin/ or some other repository for commonly used UNIX tools in your environment. You will typically require administrator (e.g. “root” or “sudo”) privileges to copy to usr/local/bin/. If in doubt, contact you system administrator for help.

[Jan_R]

If the directory is not in your path environment you should put it there. This way you do not have to specify it when you type in the commands.

In .bashrc insert a new line for the directory: export PATH=/path/to/your/directory:$PATH