Install samtools from source instead of apt, as part of #589.

Needed after upgrading Ubuntu to 20.04.
cfe-lab · Jun 23, 2021 · 8d647de · 8d647de
1 parent 52f159c
commit 8d647de
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
@@ -28,11 +28,17 @@ jobs:
 
       - name: Install IVA assembler
         run: |
-          sudo apt-get install -y zlib1g-dev libncurses5-dev libncursesw5-dev mummer samtools ncbi-blast+
+          sudo apt-get install -y zlib1g-dev libncurses5-dev libncursesw5-dev mummer ncbi-blast+
           cd ~/bin
           wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc
           wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc_dump
           chmod +x kmc kmc_dump
+          wget -q https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
+          tar -xf samtools-1.3.1.tar.bz2 --no-same-owner --bzip2
+          cd samtools-1.3.1
+          ./configure --prefix=$HOME
+          make
+          make install
           cd ~
           wget -q http://downloads.sourceforge.net/project/smalt/smalt-0.7.6-bin.tar.gz
           tar -xzf smalt-0.7.6-bin.tar.gz