From 31737a74c4360926bebf8875c17bc90eab49ccf7 Mon Sep 17 00:00:00 2001
From: Ajay Khanna <appliedstochastics@gmail.com>
Date: Thu, 7 Oct 2021 15:33:16 -0500
Subject: [PATCH] Copy test data to container and update documentation

---
 Dockerfile |  3 +++
 README.md  | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++---
 2 files changed, 72 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d54d6a7..0b9e5ad 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -39,8 +39,11 @@ LABEL \
 RUN apt-get update
 
 RUN mkdir -p /opt/bam-readcount/bin
+RUN mkdir -p /opt/bam-readcount/test-data
 WORKDIR /opt/bam-readcount
 COPY --from=0 /bam-readcount/build/bin/bam-readcount /opt/bam-readcount/bin/bam-readcount
+COPY --from=0 /bam-readcount/test-data/ref.* /opt/bam-readcount/test-data/
+COPY --from=0 /bam-readcount/test-data/test.bam* /opt/bam-readcount/test-data/
 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 1c8551d..c2e29d8 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,32 @@
 docker-bam-readcount
 ====================
 
-Docker image for `bam-readcount`
+Docker image based on Ubuntu Focal with `bam-readcount` `v1.0.0` built
+and installed. Note that this does *not* build from `master`, but the
+`v1.0.0` tag. Edit the `Dockerfile` to use `master` or a different branch
+or tag.
 
+This image is automatically built in DockerHub: https://hub.docker.com/r/mgibio/bam-readcount
 
-Usage
------
+    docker pull mgibio/bam-readcount
+
+The `bam-readcount` binary is installed as
+
+    /usr/bin/bam-readcount
+
+
+Resources
+---------
+
+https://github.com/genome/bam-readcount  
+`bam-readcount` source and documentation
+
+https://docs.docker.com/  
+Docker documentation
+
+
+Usage (via `ENTRYPOINT`)
+------------------------
 
 The Dockerfile sets
 
@@ -13,5 +34,50 @@ The Dockerfile sets
 
 so the container can be run as an executable.
 
+For example, to run `bam-readcount` on a FASTA reference `REFERENCE` and
+BAM file `BAMFILE` in the current working directory, you can do
+
+    # --rm 
+    # Remove container when done
+    # -v $(pwd):$(pwd)
+    # Maps the current working directory to the same path inside the container
+    # -w $(pwd) 
+    # Sets the working directory to the current working directory inside
+    # the container
+    docker run --rm -v $(pwd):$(pwd) -w $(pwd) mgibio/bam-readcount -f REFERENCE BAMFILE
+
+
+Usage (interactive)
+-------------------
+
+The `ENTRYPOINT` can be overridden for interactive use. 
+
+For example, to run `bam-readcount` on test data included in the container,
+do
+
+    # --rm 
+    # Remove container when done
+    # -it
+    # Docker interactive flags
+    # --entrypoint /bin/bash
+    # Set the Bash shell as the entrypoint
+    docker run --rm -it --entrypoint /bin/bash mgibio/bam-readcount
+
+The container will present an interactive prompt, and the working directory
+will be `/opt/bam-readcount`. There is a directory `test-data` there, and 
+`bam-readcount` can be run on this data with 
+
+    # -w1 
+    # The test BAM does not have the SM tag; -w1 will report warnings 
+    # only once to avoid a warning for each read
+    root@3a0a8df8b278:/opt/bam-readcount# bam-readcount -w1 -f test-data/ref.fa test-data/test.bam
+
+To make your own data available for interactive use within the container,
+use the Docker `-v` and `-w` flags to map your local directories and 
+set a working directory, for example to use the current working local 
+directory
+
+    docker run --rm -it -v $(pwd):$(pwd) -w $(pwd) --entrypoint /bin/bash mgibio/bam-readcount
+