bedtools

Bedtools is a fast, flexible toolset for genome arithmetic.

• Version: 2.29.0
• Added: January, 2013
• Updated: September, 2019
• Link: https://bedtools.readthedocs.io/en/latest/

See which versions of bedtools are available:

$ module avail bedtools

Load one version into your environment and run it:

$ module load bedtools/2.29.0
$ bedtools

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz
$ tar xf bedtools-2.29.0.tar.gz
$ cd bedtools2
# added in 2023-02 while re-compiling on CentOS Stream 8
$ sed -i 's/python/python3/' Makefile
$ make
$ sudo mkdir -p /export/apps/bedtools/2.29.0
$ sudo chown aorth /export/apps/bedtools/2.29.0
$ make install prefix=/export/apps/bedtools/2.29.0
$ sudo chown -R root:root /export/apps/bedtools/2.29.0