Makefiles to standardize running Treehouse pipelines at partner sites.
Requirments: Docker 1.12.1, 40G Memory, 100G Storage per Sample
Install and Test:
git clone https://github.com/UCSC-Treehouse/pipelines.git
cd pipelines/rnaseq-cgl-pipeline
make
Reference files will be downloaded into inputs/, a test file processed and the output verified. After about 20 minutes you should see:
TEST/RSEM/rsem.genes.norm_counts.tab
-: OK
To process your own samples place a tar file per sample in samples/ consisting of two paired read fastq's with standard R1 R2 naming and then:
make run
Intermediate files will be stores in outputs/ with the final output named after the input filename with .gz on the end. A typical single sample running on a 16 core 120G server will take about 8 hours to process. Additional samples submitted at the same time will take a bit less.
See https://github.com/BD2KGenomics/cgl-docker-lib/tree/master/rnaseq-cgl-pipeline for more details.