Typical Unix-like environment with basic development tools - all other dependencies will be fetched automatically.

• curl
• gzip
• gcc
• GNU make

These tools should be part of every Linux distribution.

• automatic dependency injection with Makefile rules, e.g. the dependency BWA is only downloaded & compiled if needed
• fully automated installation of required tools from their source
• if possible, wildcard patterns instead of rules (e.g. .bwt runs bwt)
• make will generate a dependency chain for our data and regenerate outdated files
• be able to run the newest, latest software on any machine
• use versioning for all dependencies to all reproducibility
• use make -j8 (will automatically parallelize wherever possible)

• we must be able to run the newest software on old clusters, hence everything needs to be built from scratch
• some software licenses don't allow binary releases (GATK)
• we need to be able to inspect & modify the source code
• we want to understand every bit of out pipeline
• if something doesn't build, it's outdated anyhows

Dependencies are automatically generated, e.g.

• bwa -> bwt files
• mason_variator needs fai
• GATK needs fai and dict

• build: all required build tools and source code of required programs
• data: all experimental results
• debug: temporary folder that is used to print some debug information for tests
• perm: permanent data that shouldn't be deleted
• progs: all required executables of the pipeline
• src: this pipeline's source code

• make all: runs the entire pipeline
• make test: runs D unittests

Pick out any intermediate file in the pipeline and run make <file> to generate it

• due to limitations in the Makefile the working directory must be the directory of this Makefile
• the folder names are coded statically on purpose

• BAM Reader performance test