scwalls/gostripes_sing

A repo with the minimum amount of material needed for running GoSTRIPEs

Instructions for setting up GoSTRIPEs analysis using Singularity

0. Follow instructions on GoSTRIPEs: https://github.com/BrendelGroup/GoSTRIPES/blob/master/HOWTO.md
1. Clone GoSTRIPEs_sing to your system: git clone https://github.com/rtraborn/GoSTRIPES_sing
2. Put fastqs and genome directory in your analysis directory as described in the above HOWTO.md. Specifically, add the fastq files (with the .fq suffix) to the downloads folder, and create a new genome folder inside the STRIPES/ directory.
3. Clone the Singularity image in your STRIPES/ directory as follows: singularity pull --name gostripes.simg shub://BrendelGroup/GoSTRIPES.
4. Make a project directory for each replicate and cp Makefile into it.
5. Edit makefile (in STRIPES) as needed to run the analysis.
6. Submit the job script launch_job.sh (edit the source line as needed and change headers if using non-TORQUE submission system.)