Install Haploflow on CI

cfe-lab · Sep 19, 2023 · cb1b2d3 · cb1b2d3
1 parent 138dcb2
commit cb1b2d3
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diff --git 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
@@ -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 \