ILRI Research Computing

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====== bedtools ======

Bedtools is a fast, flexible toolset for genome arithmetic.

===== Information =====

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

===== Usage =====

See which versions of bedtools are available:
<code>$ module avail bedtools</code>

Load one version into your environment and run it:
<code>$ module load bedtools/2.29.0
$ bedtools</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>