From dcfaa06e082845a225da7be17e82d43ae126e4f5 Mon Sep 17 00:00:00 2001
From: Ricky Magner <81349869+rickymagner@users.noreply.github.com>
Date: Tue, 19 Mar 2024 13:54:03 -0400
Subject: [PATCH] Update README to include list of popular software included in
 docker image (#8745)

* Update README to include list of popular software included in docker image
---
 README.md                          | 29 +++++++++++++++++++++++++++++
 scripts/docker/gatkbase/Dockerfile |  1 +
 scripts/gatkcondaenv.yml.template  |  2 ++
 3 files changed, 32 insertions(+)

diff --git a/README.md b/README.md
index 1dc2bb366b8..26e731c26db 100644
--- a/README.md
+++ b/README.md
@@ -19,6 +19,7 @@ releases of the toolkit.
 * [Requirements](#requirements)
 * [Quick Start Guide](#quickstart)
 * [Downloading GATK4](#downloading)
+  * [Tools Included in Docker Image](#dockerSoftware)
 * [Building GATK4](#building)
 * [Running GATK4](#running)
     * [Passing JVM options to gatk](#jvmoptions)
@@ -115,6 +116,34 @@ You can download and run pre-built versions of GATK4 from the following places:
 * You can download a GATK4 docker image from [our dockerhub repository](https://hub.docker.com/r/broadinstitute/gatk/). We also host unstable nightly development builds on [this dockerhub repository](https://hub.docker.com/r/broadinstitute/gatk-nightly/).
     * Within the docker image, run gatk commands as usual from the default startup directory (/gatk).
 
+### <a name="dockerSoftware">Tools Included in Docker Image</a>
+
+Our docker image contains the following bioinformatics tools, which can be run by invoking the tool name from the command line:
+* bedtools (v2.30.0)
+* samtools (1.13)
+* bcftools (1.13)
+* tabix (1.13+ds)
+
+We also include an installation of Python3 (3.6.10) with the following popular packages included:
+* numpy
+* scipy
+* tensorflow
+* pymc3
+* keras
+* scikit-learn
+* matplotlib
+* pandas
+* biopython
+* pyvcf
+* pysam
+
+We also include an installation of R (3.6.2) with the following popular packages included:
+* data.table
+* dplyr
+* ggplot2
+
+For more details on system packages, see the GATK [Base Dockerfile](scripts/docker/gatkbase/Dockerfile) and for more details on the Python3/R packages, see the [Conda environment setup file](scripts/gatkcondaenv.yml.template). Versions for the Python3/R packages can be found there.
+
 ## <a name="building">Building GATK4</a>
 
 * **To do a full build of GATK4, first clone the GATK repository using "git clone", then run:**
diff --git a/scripts/docker/gatkbase/Dockerfile b/scripts/docker/gatkbase/Dockerfile
index 7b758d19829..201ff3c6237 100644
--- a/scripts/docker/gatkbase/Dockerfile
+++ b/scripts/docker/gatkbase/Dockerfile
@@ -1,5 +1,6 @@
 # Using OpenJDK 17
 # This Dockerfile does not require any files that are in the GATK4 repo.
+# NOTE: If you update the ubuntu version make sure to update the samtools/bcftools/bedtools versions in the README
 FROM ubuntu:22.04
 
 # Avoid interactive prompts during apt installs/upgrades
diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template
index a87b2acdda3..75284b829e8 100644
--- a/scripts/gatkcondaenv.yml.template
+++ b/scripts/gatkcondaenv.yml.template
@@ -10,6 +10,8 @@
 # used by the testGATKPythonEnvironmentPackagePresent test in PythonEnvironmentIntegrationTest needs to be updated
 # to reflect the changes.
 #
+# NOTE: If you update any of the packages below, please make sure the main README is up to date with the latest package install information.
+#
 name: $condaEnvName
 channels:
 # if channels other than conda-forge are added and the channel order is changed (note that conda channel_priority is currently set to flexible),