Add sniffles

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
+  - <https://github.com/fritzsedlazeck/Sniffles>
+  - <https://github.com/MillironX/singularity-builds>