Case study workflows for SciPipe

A few case study workflows for the SciPipe publication.

Usage

1. Navigate into each of the case study workflow folders.

2. Execute the run.sh script:

./run.sh

Prerequisites

All workflows require:

• A unix like operating system (Linux or Mac)
• The Go tool chain.
  • See this link for instructions on downloading and installing Go.

The cancer analysis, and RNA-seq workflows require a few bioinformatics tools and libraries installed on the system:

• libgomp1
• python 2.7.x
• markupsafe

On Ubuntu, these can be installed with this command:

sudo apt-get install libgomp1 python
sudo pip install markupsafe

The RNA-Seq workflow requires Python 2.7.x, for the final step (running MultiQC).

Resource requirements

The RNA-seq and Drug Discovery workflows should be runnable on a reasonably modern laptop with at least a few GB of storage available.

The Cancer analysis workflow on the other hand, requires a large amount of RAM memory, at least 16GB.

The number of cores used, can be modified on each of the workflows, by editing the run.sh script and adding or modifying the -taxtasks [n] flag. E.g:

go run workflow.go -maxtasks 4

or

go build -o workflow
./workflow -maxtasks 4