From 220653a5837c0f3dd126d857f48426301a886967 Mon Sep 17 00:00:00 2001
From: Ajay Khanna <appliedstochastics@gmail.com>
Date: Fri, 23 Jul 2021 13:26:42 -0500
Subject: [PATCH 1/2] Add files for v1.0.0

---
 Dockerfile | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 README.md  | 19 +++++++++++++++++--
 2 files changed, 63 insertions(+), 2 deletions(-)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..d54d6a7
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,46 @@
+FROM ubuntu:focal
+MAINTAINER Ajay Khanna <appliedstochastics@gmail.com>
+
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NONINTERACTIVE_SEEN true
+
+# Requirements
+RUN apt-get update && \
+    # Required build tools  
+    apt-get install -y build-essential cmake && \
+    # Need git to fetch the repository
+    apt-get install -y git && \
+    # Clean up
+    apt-get clean all && \
+    rm -rf /var/lib/apt/lists/* && rm -rf /tmp/* && rm -rf /var/tmp/*
+
+# Clone and build v1.0.0
+RUN cd / && \
+    git clone https://github.com/genome/bam-readcount && \
+    cd bam-readcount && \
+    # For a specific tag enable the git checkout below
+    git checkout v1.0.0 && \
+    rm -rf build && \
+    mkdir build && \
+    cd build && \
+    cmake .. && \
+    make
+
+
+FROM ubuntu:focal
+
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NONINTERACTIVE_SEEN true
+
+LABEL \
+    version="v1.0.0" \
+    description="Ubuntu Focal with bam-readcount v1.0.0"
+
+RUN apt-get update
+
+RUN mkdir -p /opt/bam-readcount/bin
+WORKDIR /opt/bam-readcount
+COPY --from=0 /bam-readcount/build/bin/bam-readcount /opt/bam-readcount/bin/bam-readcount
+RUN ln -s /opt/bam-readcount/bin/bam-readcount /usr/bin/bam-readcount
+
+ENTRYPOINT ["/usr/bin/bam-readcount"]
diff --git a/README.md b/README.md
index 6f7293e..732b1d7 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,17 @@
-# docker-bam-readcount
-Docker containerization for "bam-readcount"
+docker-bam-readcount
+====================
+
+Docker image for `bam-readcount`
+
+
+Usage
+-----
+
+The Dockerfile sets
+
+  ENTRYPOINT ["/usr/bin/bam-readcount"]
+
+so the container can be run as an executable.
+
+
+

From 04a9d0bfc51424adae26666e38f35dfc3fc68c82 Mon Sep 17 00:00:00 2001
From: Ajay Khanna <appliedstochastics@gmail.com>
Date: Fri, 23 Jul 2021 13:28:17 -0500
Subject: [PATCH 2/2] Fix Markdown formatting

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 732b1d7..1c8551d 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ Usage
 
 The Dockerfile sets
 
-  ENTRYPOINT ["/usr/bin/bam-readcount"]
+    ENTRYPOINT ["/usr/bin/bam-readcount"]
 
 so the container can be run as an executable.