From 96f14100569e81668f87e03df61550ae2d3b8dbf Mon Sep 17 00:00:00 2001
From: MillironX <25492070+MillironX@users.noreply.github.com>
Date: Tue, 10 Aug 2021 17:35:08 -0500
Subject: [PATCH] Change sniffles base image

---
 sniffles/README.md    |  2 +-
 sniffles/sniffles.def | 32 ++++++++++++++++----------------
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/sniffles/README.md b/sniffles/README.md
index d4f3ef2..e3c59f0 100644
--- a/sniffles/README.md
+++ b/sniffles/README.md
@@ -4,7 +4,7 @@
 [![Sniffles source](https://img.shields.io/static/v1?label=Sniffles%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/fritzsedlazeck/Sniffles)
 [![Version 1.0.12b](https://img.shields.io/static/v1?label=Latest%20version&message=v1.0.12b&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/sniffles)
 [![Docs](https://img.shields.io/static/v1?label=Docs&message=wiki&color=blue&style=flat-square)](https://github.com/fritzsedlazeck/Sniffles/wiki)
-[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/)
+[![Debian base](https://img.shields.io/static/v1?label=Base%20image&message=Debian&color=a80030&logo=debian&style=flat-square)](https://www.alpinelinux.org/)
 
 Sniffles is a structural variation caller using third generation sequencing
 (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using
diff --git a/sniffles/sniffles.def b/sniffles/sniffles.def
index 95cdbcc..cddc7e2 100644
--- a/sniffles/sniffles.def
+++ b/sniffles/sniffles.def
@@ -1,20 +1,19 @@
 Bootstrap: library
-From: default/alpine:3.14.0
+From: default/debian:buster
 
 %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
+  # Install dependencies
+  apt-get update
+  apt-get install -y --no-install-recommends \
+    git cmake make gcc g++ libghc-zlib-dev bash procps build-essential
 
   # Get Sniffles
   cd /opt || exit 1
+  git config --global http.sslverify false
   git clone https://github.com/fritzsedlazeck/Sniffles.git
   cd Sniffles || exit 1
   git checkout $SNIFFLES_TAG
@@ -24,16 +23,17 @@ From: default/alpine:3.14.0
   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
+  # 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
-
-%environment
-  export SNIFFLES_VERSION='1.0.12'
-  export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
-  export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH
+  rm -rf /var/lib/apt/lists/*
 
 %test
   command -v bash
@@ -47,7 +47,7 @@ From: default/alpine:3.14.0
 %labels
   Author 25492070+MillironX@users.noreply.github.com
   SoftwareVersion v1.0.12b
-  SingularityDefinitionVersion 2
+  SingularityDefinitionVersion 3
 
 %help
   Sniffles