cgpipe - minimum viable HPC pipeline
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
blib
docs
lib
src
.gitignore
INCLUDES
LICENSE
README.md
build.xml
build_docs.sh
test.sh

README.md

cgpipe - minimum viable pipeline

Make for HPC analysis pipelines

CGPipe is a replacement for the venerable "make" that aims to automate the process of running complex analysis pipelines on high-throughput clusters. Make is a standard build tool for compiling software. The power of make is that it takes a set of instructions for building various files, and given a target output, make will determine what commands need to be run in order to build those outputs. It basically answers the questions: what inputs are needed? and how do I build those inputs? CGPipe aims to perform a similar function for pipelines that run on high-throughput/performance clusters. These pipelines can be quite elaborate, but by focusing on specific transformations, you can make the pipeline easier to create and run.

Make is a powerful tool, but it is sometimes difficult to integrate into bioinformatics pipelines. Bioinformatics pipelines are typically run on an HPC/HTC cluster using a batch scheduler. Each job could have different IO, memory, or CPU requirements. Finally, each pipeline could have to run on different clusters. Currently, only SGE/OGE and Grid Engine derivatives include a grid-aware make replacement. However, it is primarily aimed at directly building Makefiles, and that is somewhat limiting for more complicated pipelines.

CGPipe is designed to run jobs that don't span multiple nodes. Most bioinformatics pipelines require simple programs that execute on one node with one or more threads. More complicated, multi-node jobs (MPI), are likely better suited with custom execution scripts. We are willing to accept patches to better support multi-node jobs, but don't have a lot of internal experience with them.

See here for more documentation, including language specifics: https://github.com/compgen-io/cgpipe/tree/master/docs