CLONE

If you need to build the package yourself for your own version of bedtools, first clone the git repository. From the command line, type:

git clone https://github.com/PhanstielLab/bedtoolsr.git

BUILD

To build the package, run the Python script makePackage.py , located inside the bedtoolsr repository dev folder. Command-line arguments specify the path to bedtools that you want to use, the output directory, and the version suffix of the package:

usage: makePackage.py [-h] [-B BEDTOOLS] [-O OUTPUT] [-V VERSION]
optional arguments:
  -h, --help            show this help message and exit
  -B BEDTOOLS, --bedtools BEDTOOLS
                        path to your bedtools
  -O OUTPUT, --output OUTPUT
                        directory to write package to
  -V VERSION, --version VERSION
                        version number of package

Unit tests will automatically be run after the package is built. If successful, you should see something like this:

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0

python makePackage.py

FILES

The resulting package directory should contain tests in inst/tests (because they are copied here, they will be installed with the package such that unit testing can confirm functionality, as discussed here ), documentation in man , and code files in R .

Then install by opening R and typing:
install.packages("/path/to/bedtools_yourversion", type="source", repos=NULL)
More details can be found here . +1 608 609-8377 | douglas_phanstiel@med.unc.edu 3300 Thurston Building, Chapel Hill, NC 27599-7280