diff --git a/sniffles/sniffles.def b/sniffles/sniffles.def new file mode 100644 index 0000000..9761bbe --- /dev/null +++ b/sniffles/sniffles.def @@ -0,0 +1,63 @@ +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 + git clone https://github.com/fritzsedlazeck/Sniffles.git + cd Sniffles || exit 1 + git checkout $SNIFFLES_TAG + + # Build Sniffles + mkdir build && cd build || exit 1 + cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local + make + + # Install Sniffles + cd ../bin/sniffles-core-$SNIFFLES_VERSION || exit 1 + install -D -m 0755 sniffles -t /usr/local/bin + install -D -m 0755 sniffles-debug -t /usr/local/bin + + # Cleanup repo + cd ../.. || exit 1 + rm -rf Sniffles + + # Cleanup packages + apk del --no-cache .build-deps + +%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 1 + +%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 + - + -