wbazant

Singularity container for an R module on a research cluster for VEuPathDB

Introduction

To use this technology, we need Singularity installed in the target environment by root, which is possibly the largest obstacle for us.

Writing a development container

Here is a container for analysing 16s rRNA data in MicrobiomeDB, requiring an R package DADA2. DADA2 releases to BioConductor, but we want the ability to load an arbitrary commit for development.

We can build on somebody's container with r-devtools, and add our libraries:

ihnorton

m-radzikowski

#!/usr/bin/env bash

set -Eeuo pipefail
trap cleanup SIGINT SIGTERM ERR EXIT

script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P)

usage() {
  cat <<EOF
Usage: $(basename "${BASH_SOURCE[0]}") [-h] [-v] [-f] -p param_value arg1 [arg2...]

tdhopper

# http://editorconfig.org/#file-format-details
root = true

[*]
charset = utf-8
end_of_line = lf
indent_size = 4
indent_style = space
insert_final_newline = true
trim_trailing_whitespace = true

vals