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Update README to include list of popular software included in docker image #8745

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29 changes: 29 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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:**
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1 change: 1 addition & 0 deletions scripts/docker/gatkbase/Dockerfile
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@@ -1,5 +1,6 @@
# Using OpenJDK 17
# This Dockerfile does not require any files that are in the GATK4 repo.
# NOTE: If you updated 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
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2 changes: 2 additions & 0 deletions scripts/gatkcondaenv.yml.template
Original file line number Diff line number Diff line change
Expand Up @@ -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),
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