fur

Author

Bernhard Haubold, [email protected]

Description

Find unique genomic regions.

Dependencies

Building fur requires a number of packages, the Go compiler, and the two programs macle & phylonium.

• Install packages
  $ sudo apt install autoconf build-essential cmake git gnuplot libbsd-dev libbsd0 libdivsufsort-dev libdivsufsort3 libgsl-dev libgsl23 libsdsl-dev libsdsl3 ncbi-blast+ noweb primer3 sudo texlive-latex-extra texlive-latex-recommended texlive-pstricks texlive-fonts-extra texlive-science wget
• Install Go compiler
  • Download package
    $ curl https://go.dev/dl/go1.17.6.linux-amd64.tar.gz -o go1.17.6.linux-amd64.tar.gz
  • Remove old installation
    $ sudo rm -rf /usr/local/go
  • Unpack and install
    $ sudo tar -C /usr/local -xzf go1.17.6.linux-amd64.tar.gz
  • Add /usr/local/bo/bin to the PATH environment variable by adding, for example, export PATH=$PATH:/usr/local/bo/bin to $HOME/.profileand update the system by executing
    $ source $HOME/.profile
  • Verify Go installation
    $ go version
• Install macle
• Install phylonium

Compile

• Compile fur
$ make
  All executables are now in the directory build

Documentation

The command
$ make doc
generates the manual doc/fur.pdf

Docker Container

As an alternative to building fur, we also post it as a docker container. The container includes all programs needed to work through the tutorial at the end of the documentation in ~/fox.pdf.

• $ docker pull haubold/fox
• $ docker container run --detach-keys="ctrl-@" -h fox -it haubold/fox

License

GNU General Public License