From 46b3b7133454d8533aa90234da7283409d8cbbe5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6kalp=20=C3=87elik?= <37572619+gokalpcelik@users.noreply.github.com> Date: Mon, 18 Nov 2024 22:45:46 +0300 Subject: [PATCH 1/4] Update README.md Small changes to toolkit versions that are compatible with the latest release 4.6.1.0 --- README.md | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index b6300d9b6ee..ce308903ea3 100644 --- a/README.md +++ b/README.md @@ -56,11 +56,10 @@ releases of the toolkit. * Java 17 is needed to run or build GATK. We recommend one of the following: * Download the Eclipse Foundation's distribution of OpenJDK 17 from [adoptium.net](https://adoptium.net/). Navigate to the [release archive](https://adoptium.net/temurin/archive/?version=17) to find downloads for Java 17. - * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew tap homebrew/cask-versions` followed by `brew install --cask temurin17` to install the Eclipse Foundation's OpenJDK 17. - * Python 2.6 or greater (required to run the `gatk` frontend script) - * Python 3.6.2, along with a set of additional Python packages, is required to run some tools and workflows. + * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew tap homebrew/cask-versions` followed by `brew install --cask temurin17` to install the Eclipse Foundation's OpenJDK 17. + * Python 3.10.13, along with a set of additional Python packages, is required to run some tools and workflows (alsp required to run the `gatk` frontend script). See [Python Dependencies](#python) for more information. - * R 3.2.5 (needed for producing plots in certain tools) + * R 4.3.1 (needed for producing plots in certain tools) * To build GATK: * A Java 17 JDK * Git 2.5 or greater @@ -73,7 +72,7 @@ releases of the toolkit. the size of the download. * Gradle 5.6. We recommend using the `./gradlew` script which will download and use an appropriate gradle version automatically (see examples below). - * R 3.2.5 (needed for running the test suite) + * R 4.3.1 (needed for running the test suite) * Pre-packaged Docker images with all needed dependencies installed can be found on [our dockerhub repository](https://hub.docker.com/r/broadinstitute/gatk/). This requires a recent version of the docker client, which can be found on the [docker website](https://www.docker.com/get-docker). @@ -141,10 +140,10 @@ Our docker image contains the following bioinformatics tools, which can be run b * bcftools (1.13) * tabix (1.13+ds) -We also include an installation of Python3 (3.6.10) with the following popular packages included: +We also include an installation of Python3 (3.10.13) with the following popular packages included: * numpy * scipy -* tensorflow +* pytorch * pymc3 * keras * scikit-learn @@ -154,7 +153,7 @@ We also include an installation of Python3 (3.6.10) with the following popular p * pyvcf * pysam -We also include an installation of R (3.6.2) with the following popular packages included: +We also include an installation of R (4.3.1) with the following popular packages included: * data.table * dplyr * ggplot2 @@ -203,7 +202,7 @@ For more details on system packages, see the GATK [Base Dockerfile](scripts/dock ## Running GATK4 * The standard way to run GATK4 tools is via the **`gatk`** wrapper script located in the root directory of a clone of this repository. - * Requires Python 2.6 or greater (this includes Python 3.x) + * Requires Python 3.6 or greater * You need to have built the GATK as described in the [Building GATK4](#building) section above before running this script. * There are several ways `gatk` can be run: * Directly from the root of your git clone after building From 32f01b8c300c5c874bdd39506a269abd1ef91256 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6kalp=20=C3=87elik?= <37572619+gokalpcelik@users.noreply.github.com> Date: Mon, 18 Nov 2024 23:20:14 +0300 Subject: [PATCH 2/4] Update README.md Additional requested changes. --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ce308903ea3..7d5da22a841 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ releases of the toolkit. * Java 17 is needed to run or build GATK. We recommend one of the following: * Download the Eclipse Foundation's distribution of OpenJDK 17 from [adoptium.net](https://adoptium.net/). Navigate to the [release archive](https://adoptium.net/temurin/archive/?version=17) to find downloads for Java 17. - * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew tap homebrew/cask-versions` followed by `brew install --cask temurin17` to install the Eclipse Foundation's OpenJDK 17. + * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew tap homebrew/cask-versions` followed by `brew install temurin@17` to install the Eclipse Foundation's OpenJDK 17. * Python 3.10.13, along with a set of additional Python packages, is required to run some tools and workflows (alsp required to run the `gatk` frontend script). See [Python Dependencies](#python) for more information. * R 4.3.1 (needed for producing plots in certain tools) @@ -202,7 +202,7 @@ For more details on system packages, see the GATK [Base Dockerfile](scripts/dock ## Running GATK4 * The standard way to run GATK4 tools is via the **`gatk`** wrapper script located in the root directory of a clone of this repository. - * Requires Python 3.6 or greater + * Requires Python 3.9 or greater * You need to have built the GATK as described in the [Building GATK4](#building) section above before running this script. * There are several ways `gatk` can be run: * Directly from the root of your git clone after building From 93a25f08e4e2b13370263ab4572fdabb366b1794 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6kalp=20=C3=87elik?= <37572619+gokalpcelik@users.noreply.github.com> Date: Mon, 18 Nov 2024 23:21:51 +0300 Subject: [PATCH 3/4] Update README.md o instead of p --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7d5da22a841..88e986ce038 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,7 @@ releases of the toolkit. We recommend one of the following: * Download the Eclipse Foundation's distribution of OpenJDK 17 from [adoptium.net](https://adoptium.net/). Navigate to the [release archive](https://adoptium.net/temurin/archive/?version=17) to find downloads for Java 17. * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew tap homebrew/cask-versions` followed by `brew install temurin@17` to install the Eclipse Foundation's OpenJDK 17. - * Python 3.10.13, along with a set of additional Python packages, is required to run some tools and workflows (alsp required to run the `gatk` frontend script). + * Python 3.10.13, along with a set of additional Python packages, is required to run some tools and workflows (also required to run the `gatk` frontend script). See [Python Dependencies](#python) for more information. * R 4.3.1 (needed for producing plots in certain tools) * To build GATK: From 7966ae4c93de650241067ace9db98ba8bae2ce61 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 19 Nov 2024 12:16:31 -0500 Subject: [PATCH 4/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 88e986ce038..7f570e52f78 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ releases of the toolkit. * Java 17 is needed to run or build GATK. We recommend one of the following: * Download the Eclipse Foundation's distribution of OpenJDK 17 from [adoptium.net](https://adoptium.net/). Navigate to the [release archive](https://adoptium.net/temurin/archive/?version=17) to find downloads for Java 17. - * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew tap homebrew/cask-versions` followed by `brew install temurin@17` to install the Eclipse Foundation's OpenJDK 17. + * On Mac OS, you can install the [Homebrew package manager](https://brew.sh/) and run `brew install temurin@17` to install the Eclipse Foundation's OpenJDK 17. * Python 3.10.13, along with a set of additional Python packages, is required to run some tools and workflows (also required to run the `gatk` frontend script). See [Python Dependencies](#python) for more information. * R 4.3.1 (needed for producing plots in certain tools)