eppic-pipeline

Main repository of scripts for running EPPIC 3, generally with the intent of generating data for the web server.

EPPIC support the following use cases:

1. Local EPPIC database & server with minimal set of test cases
2. Pipeline to compute the full PDB
3. Topup pipeline to keep an existing installation up-to-date

Organization

• config Configuration variables. Be careful about checking things in here
• docker Scripts for building docker images, if any
• scripts All scripts for running EPPIC
  • local Scripts for directly running EPPIC locally on a small set of jobs
  • pipeline Scripts for PDB-wide analysis. Depends on local scripts
    • dev Scripts that should be run on the dev server
    • sge Scripts intended to be run on a cluster running Sun Grid Engine
    • web Scripts to run on the production web server
  • topup Scripts for augmenting a PDB-wide analysis. Depends on local and pipeline scripts
  • unmigrated Raw scripts collected from various hosts. These are intended to be organized into the other folders over time.

Configuration

All paths and external resources are configured through config/pipeline.conf.

Passwords are stored in config/credentials.conf, which can be copied from the example

Workflows

Misc notes

# sync merlin results back to local
rsync -av merlinl01:/gpfs/home/bliven_s/eppic-3.0/output/data  /data/spencer/eppic/wui/files3_2016_05_test