diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..25bf2bd
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,31 @@
+bin
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..a8cd6ca
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,78 @@
+# Build modwt
+FROM alpine:3.7 as modwt-build
+RUN apk add --no-cache \
+  g++ \
+  git \
+  make
+RUN git clone https://github.com/StamLab/modwt.git \
+      && cd modwt \
+      && git checkout 28e9f479c737836ffc870199f2468e30659ab38d \
+      && make
+
+# Build samtools
+FROM alpine:3.7 as samtools-build
+RUN apk add --no-cache \
+    autoconf \
+    g++ \
+    git \
+    bzip2-dev \
+    make \
+    ncurses-dev \
+    xz-dev \
+    zlib-dev
+RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 \
+      && tar xf samtools-1.7.tar.bz2 \
+      && cd samtools-1.7 \
+      && make install
+
+# Build hotspot2
+FROM alpine:3.7 as hotspot2-build
+RUN apk add --no-cache \
+      bash \
+      g++ \
+      make
+WORKDIR /hotspot2
+ADD . .
+RUN make
+
+# Build bedGraphToBigWig
+FROM alpine:3.7 as kentutils-build
+RUN apk add --no-cache \
+      g++ \
+      gcc \
+      git \
+      libpng-dev \
+      make \
+      mysql-dev \
+      zlib-dev
+# Get an archive of kentUtils, remove a file that doesn't build, and compile
+RUN wget https://github.com/ENCODE-DCC/kentUtils/archive/v302.0.0.tar.gz \
+      && tar xf v302.0.0.tar.gz \
+      && cd kentUtils-302.0.0 \
+      && sed -i 's/fof.o //' src/lib/makefile \
+      && make
+
+# Build the final container
+FROM alpine:3.7 as hotspot2
+# Install dynamic libraries
+RUN apk add --no-cache \
+      bash \
+      bc \
+      bzip2-dev \
+      coreutils \
+      ncurses \
+      xz-dev \
+      zlib-dev
+# Get bedops
+RUN wget -O - https://github.com/bedops/bedops/releases/download/v2.4.31/bedops_linux_x86_64-v2.4.31.tar.bz2 \
+  | tar -C /usr/local -xjf -
+# Get built files
+COPY --from=kentutils-build /kentUtils-302.0.0/bin/bedGraphToBigWig /usr/local/bin/
+COPY --from=kentutils-build /kentUtils-302.0.0/bin/bedToBigBed /usr/local/bin/
+
+COPY --from=modwt-build /modwt/bin/ /usr/local/bin/
+
+COPY --from=samtools-build /usr/local/bin /usr/local/bin/
+
+COPY --from=hotspot2-build /hotspot2/bin/ /usr/local/bin/
+COPY --from=hotspot2-build /hotspot2/scripts/ /usr/local/bin/