whbrewer / mendel-f90

Original Fortran 90 implementation of Mendel's Accountant.

README

Note: this is the original/old version of Mendel's Accountant implemented in Fortran. This is not used anymore. It is kept here for reference.

Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine.

For more information visit http://www.mendelsaccountant.info or http://sourceforge.net/projects/mendelsaccount

INSTALLATION

• Build instructions: (1) edit Makefile, (2) run "make"

• A Fortran compiler is required for compiling. A free gfortran compile can easily by installed on a Linux system by executing the command sudo apt-get install gfortran on Debian/Ubuntu systems, and sudo yum install gfortran on Redhat/Centos/SuSe systems.

• gfortran can also easily on Mac OS X using Homebrew (see brew.sh) by running brew install gcc (gfortran is included with gcc). You'll also need to install two files: libmpfr.4.dylib and libmpc.3.dylib in /usr/local/lib.

• MPICH (optional). Since mendel uses mpich libraries, for parallel computations, you may download and install mpich from www.mpich.org/downloads/.

• However, it is possible to install mendel without installing the parallel libs, which means all options will work, but will be limited to running a single tribe/deme at a time. In order to compile Mendel without the parallel libs, first remove all MPICH code by running "make preserial", then run "make serial". It will croak when it tries to do the final linking. So run this command after it fails:

gfortran -O3 -I/usr/local/include -static-libgfortran -static-libgcc -o mendel_serial sort.o random_pkg.o inputs.o genome.o profile.o polygenic.o selection.o mutation.o mating.o fileio.o mendel_serial.o init_serial.o

INTERFACE

Mendel's Accountant was designed to work with the Scientific Platform for the Cloud (SPC). Instructions for setting up SPC can be found here: https://bitbucket.org/whbrewer/spc

Since SPC is based on Python 2.7 which is no longer supported, a Dockerfile is provided to build a Docker container. This assumes that Docker has first been installed from https://docker.com. The command is as follows:

docker build . -t mendel:2.7.3

Once the image has been built, the container can be started using the following command, and then run:

docker run -p 8580:8580 mendel:2.7.3

Then should be able to open a browser window to localhost:8580 to run mendel.