From b63f1125963a1deb9a062b20ac65464a250b204b Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 19 Sep 2023 11:53:52 -0700
Subject: [PATCH] Install Haploflow in Singularity

---
 Singularity | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/Singularity b/Singularity
index e32803957..55f268f3e 100644
--- a/Singularity
+++ b/Singularity
@@ -122,6 +122,18 @@ From: centos:7
     tar -xzf smalt-0.7.6-bin.tar.gz --no-same-owner
     ln -s /opt/smalt-0.7.6-bin/smalt_x86_64 /bin/smalt
 
+    ## Install Haploflow
+    yum install -y boost-devel cmake
+    cd /opt/
+    git clone https://github.com/hzi-bifo/Haploflow
+    cd Haploflow
+    git checkout 9a5a0ff6c3a0435e723e41f98fe82ec2ad19cf50
+    mkdir -p build
+    cd build
+    cmake ..
+    make
+    ln -s /opt/Haploflow/build/haploflow /bin/haploflow
+
     echo ===== Installing Python packages ===== >/dev/null
     # Also trigger matplotlib to build its font cache.
     wget -q https://bootstrap.pypa.io/get-pip.py