Running the Mummer alignment tool in a Docker container

mummer.md

Running the Mummer alignment tool in a Docker container

Project details: https://github.com/mummer4/mummer

Run a Debian Docker container

Note: I'm using Debian because Ubuntu seems to have some issues setting up Perl correctly on x86 and that can lead mummerplot to error out with "Can't locate Sys/Hostname.pm in @INC..."

$ mkdir mummer && cd mummer
$ docker run --rm -it -v$(pwd):/workspace debian bash

Inside the container

$ cd /workspace/
$ apt update && apt install -y wget
$ wget https://github.com/mummer4/mummer/releases/download/v4.0.1/mummer-4.0.1.tar.gz
$ tar -xzf mummer-4.0.1.tar.gz
$ apt install -y build-essential gnuplot swig python3-dev ruby-dev libperl-dev git yaggo autoconf automake libtool gettext
$ cd mummer-4.0.1
$ autoreconf -fi
$ mkdir -p /workspace/mummer && ./configure --prefix=/workspace/mummer
$ make
$ make check
$ make install
$ cd ../mummer/bin
$ ./mummer --version
$ ./mummerplot -h

Note: If you get errors similar to "Can't determine default terminal type at mummer/bin/mummerplot line 1512" when running mummerplot, make sure gnuplot is installed and, if yes, check if this command runs successfully: gnuplot -e “show terminal”.