From cb1b2d3d4599f6856d1df032f08799800ccc7edd Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 18 Sep 2023 17:58:33 -0700
Subject: [PATCH] Install Haploflow on CI

---
 .github/workflows/build-and-test.yml | 8 ++++++++
 Dockerfile                           | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index de5ebe481..b1a6f01f0 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -16,6 +16,14 @@ jobs:
         with:
           go-version: '^1.15.6'
 
+      - name: Install Haploflow
+        run: |
+          sudo apt-get install -qq build-essential sudo git ronn
+          cd /opt/
+          git clone https://github.com/hzi-bifo/Haploflow
+          cd /opt/Haploflow && sh build.sh
+          sudo ln -s /opt/Haploflow/build/haploflow ~/bin/haploflow
+
       - name: Install IVA assembler dependencies
         run: |
           sudo apt-get install -qq zlib1g-dev libncurses5-dev libncursesw5-dev mummer ncbi-blast+
diff --git a/Dockerfile b/Dockerfile
index cc4729cca..ca8c41ee3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -83,7 +83,7 @@ RUN apt-get install -q -y zlib1g-dev libncurses5-dev libncursesw5-dev && \
     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
 
-## Installing Haploflow
+## Install Haploflow
 RUN apt-get install -y build-essential sudo git ronn \
     cd /opt/ &&
     git clone https://github.com/hzi-bifo/Haploflow \