This is the git repository for the Code Monkeys session on GNU make and the perl library DistributedMake (DM). In this session we will build a pipeline using a bash script, a make file and a DM-based perl script. All of these methods have their advantages and disadvantages. The goal of this session is to get a hands-on understanding of what they are.
The pipeline will be borrowed from bioinformatics. Specifically, we will be aligning human Illumina sequencing reads to the human reference genome, and calling variants on the aligned reads with GATK.
You will need a UNIX like environment. Furthermore, Java JDK 7 or newer
and GCC are necessary to compile and run the programs that will be used in the
pipelines. For running the DistributedMake (DM) perl script located in
results/dm you will need perl 5.8.8 or later as well as an
installed version of the perl library
DM. DM is still experimental and
has many perl library dependencies. As such, installing DM requires
advanced perl knowledge. I highly recommend having a
working version of
cpanm
to install DM with. I believe DM version 0.13 is already installed on rescomp.
Download this git repository
git clone https://github.com/wkretzsch/code-monkeys-wwk.git
cd code-monkeys-wwk
Run the setup script. This script downloads a few large files I
deemed to large for git and compiles the programs in the src
directory
./setup.sh
Contains input data for the pipeline. See data/README.sh for when
and where the files were downloaded.
Contains the three working directories results/bash, results/make
and results/dm: one for each pipelining method.
Contains all programs needed to perform the steps of the pipeline.
Compiled binaries are stored in bin for reference by the pipelines.