yapp (yet another pplacer pipeline)

overview

A pplacer pipleine with the following features and objectives:

• intended to contain only a single project
• flat (actions are mostly basic scons Commands without functional wrappers)
• optionally uses bioscons for dispatch to the cluster using Slurm
• creates an execution environment that relies on local copies of many dependencies
• supports Infernal 1.1

Requirements

• Apptainer/Singularity
• Python 3
• SQLite

execution

After cloning and entering the repository:

# Install Apptainer/Singularity and SQLite
ml Apptainer SQLite
cp settings-example.conf settings.conf
# modify settings.conf as necessary
# Install Python dependencies
bin/setup.sh
source yapp-env/bin/activate

Execute the pipeline:

scons -f SConstruct-get-data
scons
scons -f SConstruct-get-details && scons -f SConstruct-get-details

Docker image

This project provides a Docker container hosted on ghcr.io providing a Python execution environment for some scripts. Manual build and deployment can be performed as follows:

bin/docker-build.sh
bin/docker-build.sh push

Run the container:

% docker run --platform=linux/amd64 --rm -it ghcr.io/fhcrc/yapp:latest
Python 3.11.2 (main, Mar 23 2023, 03:00:37) [GCC 10.2.1 20210110] on linux