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 - -