Bootstrap: library
From: default/alpine:3.14.0

%post
  # Declare version variable
  export SNIFFLES_VERSION='1.0.12'
  export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"

  # Install build dependencies
  apk add --no-cache --virtual .build-deps \
    git cmake make gcc g++ zlib-dev

  # Install real dependencies
  apk add --no-cache bash

  # Get Sniffles
  cd /opt || exit 1
  git clone https://github.com/fritzsedlazeck/Sniffles.git
  cd Sniffles || exit 1
  git checkout $SNIFFLES_TAG

  # Build Sniffles
  mkdir build && cd build || exit 1
  cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
  make

  # Add Sniffles to PATH
  export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH

  # Cleanup packages
  apk del --no-cache .build-deps

%environment
  export SNIFFLES_VERSION='1.0.12'
  export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
  export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH

%test
  command -v bash
  command -v ps
  command -v sniffles
  command -v sniffles-debug

%runscript
  sniffles "$@"

%labels
  Author 25492070+MillironX@users.noreply.github.com
  SoftwareVersion v1.0.12b
  SingularityDefinitionVersion 2

%help
  Sniffles
  ========

  Sniffles is a structural variation caller using third generation sequencing
  (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using
  evidence from split-read alignments, high-mismatch regions, and coverage
  analysis.

  For more help, see
  - <https://github.com/fritzsedlazeck/Sniffles>
  - <https://github.com/MillironX/singularity-builds>