Include samtools package in gwas.sif

Fixes #219

docker/scripts/install_bcftools.sh

@@ -3,13 +3,13 @@ set -euo pipefail
 
 # deps 
 apt-get update && apt-get install -y --no-install-recommends \
-    libcurl4-gnutls-dev=7.68.0-1ubuntu2.19 \
-    libperl-dev=5.30.0-9ubuntu0.4 \
+    libcurl4-gnutls-dev=7.68.0-1ubuntu2.21 \
+    libperl-dev=5.30.0-9ubuntu0.5 \
     && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-# bcfools
+# bcftools
 git clone --recurse-submodules --depth 1 -b 1.12 https://github.com/samtools/bcftools.git && \
 cd bcftools && \
 autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters --with-htslib=/usr/ && \

docker/scripts/install_htslib.sh

@@ -5,7 +5,7 @@ set -euo pipefail
 apt-get update && apt-get install --no-install-recommends \
     libbz2-dev=1.0.8-2 \
     liblzma-dev=5.2.4-1ubuntu1.1 \
-    libssl-dev=1.1.1f-1ubuntu2.19 \
+    libssl-dev=1.1.1f-1ubuntu2.20 \
     -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

docker/scripts/install_minimac4.sh

@@ -4,7 +4,7 @@ set -euo pipefail
 # install some deps for installing cget
 apt-get update && \
     apt-get install --no-install-recommends \
-    python3-pip=20.0.2-5ubuntu1.9 \
+    python3-pip=20.0.2-5ubuntu1.10 \
     python3-click=7.0-3 \
     python3-six=1.14.0-2 \
     -y && \

docker/scripts/install_samtools.sh

@@ -1,9 +1,15 @@
 #!/bin/sh
 set -euo pipefail
 
-# bcfools
+apt-get update && apt-get install -y --no-install-recommends \
+    libncurses-dev=6.2-0ubuntu2.1 \
+    && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# samtools
 git clone --depth 1 -b 1.12 https://github.com/samtools/samtools.git && \
-cd bcftools && \
+cd samtools && \
     autoheader && \
     autoconf -Wno-syntax && \
     ./configure --with-htslib=/usr/ && \