CtDNATools: A Java repository from LauraLP

This project is in a pre-release stage of development. It is subject to change without warning. Do not use this code for production work.

If you are looking for the current version of GATK to use in production work (ie., GATK3), please see the GATK website, where you can download a precompiled executable, read documentation, ask questions and receive technical support.

GATK 4

This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents of this repository are 100% open source and released under the BSD 3-Clause license (see LICENSE.TXT).

GATK4 aims to bring together well-established tools from the GATK and Picard codebases under a streamlined framework, and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using Apache Spark. It also contains many newly developed tools not present in earlier releases of the toolkit.

Requirements
Quick Start Guide
Downloading GATK4
Building GATK4
Running GATK4
For GATK Developers
Further Reading on Spark
How to contribute to GATK
Discussions
Authors
License

Requirements

Java 8
Git 2.5 or greater
Optional, but recommended:
- Gradle 3.1 or greater, needed for building the GATK. We recommend using the ./gradlew script which will download and use an appropriate gradle version automatically (see examples below).
- Python 2.6 or greater (needed for running the gatk-launch frontend script)
- R 3.1.3 (needed for producing plots in certain tools, and for running the test suite)
- git-lfs 1.1.0 or greater (needed to download large files for the complete test suite). Run git lfs install after downloading, followed by git lfs pull from the root of your git clone to download the large files. The download is several hundred megabytes.

Quick Start Guide

Build the GATK: ./gradlew bundle (creates gatk-VERSION.zip in build/)
Get help on running the GATK: ./gatk-launch --help
Get a list of available tools: ./gatk-launch --list
Run a tool: ./gatk-launch PrintReads -I src/test/resources/NA12878.chr17_69k_70k.dictFix.bam -O output.bam
Get help on a particular tool: ./gatk-launch PrintReads --help

Downloading GATK4

You can download and run pre-built versions of GATK4 from the following places:

Starting with the beta release, a zip archive with everything you need to run GATK4 can be downloaded for each release from the github releases page.
Starting with the beta release, you can download a GATK4 docker image from our dockerhub repository. We also host unstable nightly development builds on this dockerhub repository.
- Within the docker image, run gatk-launch commands as usual from the default startup directory (/gatk).

Building GATK4

To do a full build of GATK4, run:
```
  ./gradlew bundle
```
Equivalently, you can just type:
```
  ./gradlew
```
- This creates a zip archive in the build/ directory with a name like gatk-VERSION.zip containing a complete standalone GATK distribution, including our launcher gatk-launch, both the local and spark jars, and this README.
- You can also run GATK commands directly from the root of your git clone after running this command.
Other ways to build:
- ./gradlew installDist
  - Does a fast build that only lets you run GATK tools from inside your git clone, and locally only (not on a cluster). Good for developers!
- ./gradlew installAll
  - Does a semi-fast build that only lets you run GATK tools from inside your git clone, but works both locally and on a cluster. Good for developers!
- ./gradlew localJar
  - Builds only the GATK jar used for running tools locally (not on a Spark cluster). The resulting jar will be in build/libs with a name like gatk-package-VERSION-local.jar, and can be used outside of your git clone.
- ./gradlew sparkJar
  - Builds only the GATK jar used for running tools on a Spark cluster (rather than locally). The resulting jar will be in build/libs with a name like gatk-package-VERSION-spark.jar, and can be used outside of your git clone.
  - This jar will not include Spark and Hadoop libraries, in order to allow the versions of Spark and Hadoop installed on your cluster to be used.
To remove previous builds, run:
```
  ./gradlew clean
```
For faster gradle operations, add org.gradle.daemon=true to your ~/.gradle/gradle.properties file. This will keep a gradle daemon running in the background and avoid the ~6s gradle start up time on every command.
Gradle keeps a cache of dependencies used to build GATK. By default this goes in ~/.gradle. If there is insufficient free space in your home directory, you can change the location of the cache by setting the GRADLE_USER_HOME environment variable.

Running GATK4

The standard way to run GATK4 tools is via the gatk-launch wrapper script located in the root directory of a clone of this repository.
- Requires Python 2.6 or greater (this includes Python 3.x)
- You need to have built the GATK as described in the Building GATK4 section above before running this script.
- There are several ways gatk-launch can be run:
  - Directly from the root of your git clone after building
  - By extracting the zip archive produced by ./gradlew bundle to a directory, and running gatk-launch from there
  - Manually putting the gatk-launch script within the same directory as fully-packaged GATK jars produced by ./gradlew localJar and/or ./gradlew sparkJar
  - Defining the environment variables GATK_LOCAL_JAR and GATK_SPARK_JAR, and setting them to the paths to the GATK jars produced by ./gradlew localJar and/or ./gradlew sparkJar
- gatk-launch can run non-Spark tools as well as Spark tools, and can run Spark tools locally, on a Spark cluster, or on Google Cloud Dataproc.
- Note: running with java -jar directly and bypassing gatk-launch causes several important system properties to not get set, including htsjdk compression level!
For help on using gatk-launch itself, run ./gatk-launch --help
To print a list of available tools, run ./gatk-launch --list.
- Spark-based tools will have a name ending in Spark (eg., BaseRecalibratorSpark). Most other tools are non-Spark-based.
To print help for a particular tool, run ./gatk-launch ToolName --help.
To run a non-Spark tool, or to run a Spark tool locally, the syntax is: ./gatk-launch ToolName toolArguments.

Examples:

./gatk-launch PrintReads -I input.bam -O output.bam

./gatk-launch PrintReadsSpark -I input.bam -O output.bam

Passing JVM options to gatk-launch

To pass JVM arguments to GATK, run gatk-launch with the --javaOptions argument:

./gatk-launch --javaOptions "-Xmx4G" <rest of command>
 
./gatk-launch --javaOptions "-Xmx4G -XX:+PrintGCDetails" <rest of command>

Running GATK4 with inputs on Google Cloud Storage:

Many GATK4 tools can read BAM or VCF inputs from a Google Cloud Storage bucket. Just use the "gs://" prefix:
```
./gatk-launch PrintReads -I gs://mybucket/path/to/my.bam -L 1:10000-20000 -O output.bam
```
Important: You must set up your credentials first for this to work! There are three options:
- Option (a): run in a Google Cloud Engine VM
  - If you are running in a Google VM then your credentials are already in the VM and will be picked up by GATK, you don't need to do anything special.
- Option (b): use your own account
  - Install Google Cloud SDK
  - Log into your account:
```
gcloud auth application-default login
```
  - Done! GATK will use the application-default credentials you set up there.
- Option (c): use a service account
  - Create a new service account on the Google Cloud web page and download the JSON key file
  - Install Google Cloud SDK
  - Tell gcloud about the key file:
```
gcloud auth activate-service-account --key-file "$PATH_TO_THE_KEY_FILE"
```
  - Set the GOOGLE_APPLICATION_CREDENTIALS environment variable to point to the file
```
export GOOGLE_APPLICATION_CREDENTIALS="$PATH_TO_THE_KEY_FILE"
```
  - Done! GATK will pick up the service account. You can also do this in a VM if you'd like to override the default credentials.

Running GATK4 Spark tools on a Spark cluster:

./gatk-launch ToolName toolArguments -- --sparkRunner SPARK --sparkMaster <master_url> additionalSparkArguments

Examples:

./gatk-launch PrintReadsSpark -I hdfs://path/to/input.bam -O hdfs://path/to/output.bam \
    -- \
    --sparkRunner SPARK --sparkMaster <master_url>

./gatk-launch PrintReadsSpark -I hdfs://path/to/input.bam -O hdfs://path/to/output.bam \
  -- \
  --sparkRunner SPARK --sparkMaster <master_url> \
  --num-executors 5 --executor-cores 2 --executor-memory 4g \
  --conf spark.yarn.executor.memoryOverhead=600

You can also omit the "--num-executors" argument to enable dynamic allocation if you configure the cluster properly (see the Spark website for instructions).
Note that the Spark-specific arguments are separated from the tool-specific arguments by a --.
Running a Spark tool on a cluster requires Spark to have been installed from http://spark.apache.org/, since gatk-launch invokes the spark-submit tool behind-the-scenes.
Note that the examples above use YARN but we have successfully run GATK4 on Mesos as well.

Running GATK4 Spark tools on Google Cloud Dataproc:

You must have a Google cloud services account, and have spun up a Dataproc cluster in the Google Developer's console. You may need to have the "Allow API access to all Google Cloud services in the same project" option enabled (settable when you create a cluster).
You need to have installed the Google Cloud SDK from here, since gatk-launch invokes the gcloud tool behind-the-scenes. As part of the installation, be sure that you follow the gcloud setup instructions here.
Your inputs to the GATK when running on dataproc are typically in Google Cloud Storage buckets, and should be specified on your GATK command line using the syntax gs://my-gcs-bucket/path/to/my-file
You can run GATK4 jobs on Dataproc from your local computer or from the VM (master node) on the cloud.

Once you're set up, you can run a Spark tool on your Dataproc cluster using a command of the form:

./gatk-launch ToolName toolArguments -- --sparkRunner GCS --cluster myGCSCluster additionalSparkArguments

Examples:

./gatk-launch PrintReadsSpark \
    -I gs://my-gcs-bucket/path/to/input.bam \
    -O gs://my-gcs-bucket/path/to/output.bam \
    -- \
    --sparkRunner GCS --cluster myGCSCluster

./gatk-launch PrintReadsSpark \
    -I gs://my-gcs-bucket/path/to/input.bam \
    -O gs://my-gcs-bucket/path/to/output.bam \
    -- \
    --sparkRunner GCS --cluster myGCSCluster \
    --num-executors 5 --executor-cores 2 --executor-memory 4g \
    --conf spark.yarn.executor.memoryOverhead=600

When using Dataproc you can access the web interfaces for YARN, Hadoop and HDFS. Follow these instructions to create an SSH tunnel and connect with your browser.
Note that the spark-specific arguments are separated from the tool-specific arguments by a --.
If you want to avoid uploading the GATK jar to GCS on every run, set the GATK_GCS_STAGING environment variable to a bucket you have write access to (eg., export GATK_GCS_STAGING=gs://<my_bucket>/)
Dataproc Spark clusters are configured with dynamic allocation so you can omit the "--num-executors" argument and let YARN handle it automatically.

Note on 2bit Reference

Note: Some GATK Spark tools by default require the reference file to be in 2bit format (notably BaseRecalibratorSpark,BQSRPipelineSpark and ReadsPipelineSpark). You can convert your fasta to 2bit by using the faToTwoBit utility from UCSC - see also the documentation for faToTwoBit.

Using R to generate plots

Certain GATK tools may optionally generate plots if R is installed. We recommend R v3.1.3 if you want to produce plots. If you are uninterested in plotting, R is still required by several of the unit tests. Plotting is currently untested and should be viewed as a convenience rather than a primary output.

R installation is not part of the gradle build. See http://cran.r-project.org/ for general information on installing R for your system.

for ubuntu see these ubuntu specific instructions
for OSX we recommend installation through homebrew

brew tap homebrew/science
brew install R

The plotting R scripts require certain R packages to be installed. You can install these by running scripts/install_R_packages.R. Either run it as superuser to force installation into the sites library or run interactively and create a local library.

sudo Rscript scripts/install_R_packages.R

R 
source("scripts/install_R_packages.R")

Running the CNV workflows

A walkthrough and examples for the CNV workflows can be found here

Bash Command-line Tab Completion (BETA)

A tab completion bootstrap file for the bash shell is now included in releases. This file allows the command-line shell to complete GATK run options in a manner equivalent to built-in command-line tools (e.g. grep).
This tab completion functionality has only been tested in the bash shell, and is released as a beta feature.
To enable tab completion for the GATK, open a terminal window and source the included tab completion script:

source gatk-launch-completion.sh

Sourcing this file will allow you to press the tab key twice to get a list of options available to add to your current GATK command. By default you will have to source this file once in each command-line session, then for the rest of the session the GATK tab completion functionality will be available. GATK tab completion will be available in that current command-line session only.
Note that you must have already started typing an invocation of the GATK (using gatk-launch) for tab completion to initiate:

./gatk-launch <TAB><TAB>

We recommend adding a line to your bash settings file (i.e. your ~/.bashrc file) that sources the tab completion script. To add this line to your bash settings / bashrc file you can use the following command:

echo "source <PATH_TO>/gatk-launch-completion.sh" >> ~/.bashrc

Where <PATH_TO> is the fully qualified path to the gatk-launch-completion.sh script.

For GATK Developers

General guidelines for GATK4 developers

Do not put private or restricted data into the repo.
Try to keep datafiles under 100kb in size. Larger test files should go into src/test/resources/large (and subdirectories) so that they'll be stored and tracked by git-lfs as described above.
GATK4 is BSD licensed. The license is in the top level LICENSE.TXT file. Do not add any additional license text or accept files with a license included in them.
Each tool should have at least one good end-to-end integration test with a check for expected output, plus high-quality unit tests for all non-trivial utility methods/classes used by the tool. Although we have no specific coverage target, coverage should be extensive enough that if tests pass, the tool is guaranteed to be in a usable state.
All newly written code must have good test coverage (>90%).
All bug fixes must be accompanied by a regression test.
All pull requests must be reviewed before merging to master (even documentation changes).
Don't issue or accept pull requests that introduce warnings. Warnings must be addressed or suppressed.
Don't issue or accept pull requests that significantly decrease coverage (less than 1% decrease is sort of tolerable).
Don't use toString() for anything other than human consumption (ie. don't base the logic of your code on results of toString().)
Don't override clone() unless you really know what you're doing. If you do override it, document thoroughly. Otherwise, prefer other means of making copies of objects.
For logging, use org.apache.logging.log4j.Logger
We mostly follow the Google Java Style guide
Git: Don't push directly to master - make a pull request instead.
Git: Rebase and squash commits when merging.
If you push to master or mess up the commit history, you owe us 1 growler or tasty snacks at happy hour. If you break the master build, you owe 3 growlers (or lots of tasty snacks). Beer may be replaced by wine (in the color and vintage of buyer's choosing) in proportions of 1 growler = 1 bottle.

Testing GATK

Before running the test suite, be sure that you've installed git lfs and downloaded the large test data, following the git lfs setup instructions
To run the test suite, run ./gradlew test.
- Test report is in build/reports/tests/test/index.html.
- What will happen depends on the value of the TEST_TYPE environment variable:
  - unset or any other value : run non-cloud unit and integration tests, this is the default
  - cloud, unit, integration, spark : run only the cloud, unit, integration, or Spark tests
  - all : run the entire test suite
- Cloud tests require being logged into gcloud and authenticated with a project that has access to the cloud test data. They also require setting several certain environment variables.
  - HELLBENDER_JSON_SERVICE_ACCOUNT_KEY : path to a local JSON file with service account credentials
  - HELLBENDER_TEST_PROJECT : your google cloud project
  - HELLBENDER_TEST_APIKEY : your google cloud API key
  - HELLBENDER_TEST_STAGING : a gs:// path to a writable location
  - HELLBENDER_TEST_INPUTS : path to cloud test data, ex: gs://hellbender/test/resources/
- Setting the environment variable TEST_VERBOSITY=minimal will produce much less output from the test suite
To run a subset of tests, use gradle's test filtering (see gradle doc):
- You can use test.single when you just want to run a specific test class:
  - ./gradlew test -Dtest.single=SomeSpecificTestClass
- You can also use --tests with a wildcard to run a specific test class, method, or to select multiple test classes:
  - ./gradlew test --tests *SomeSpecificTestClass
  - ./gradlew test --tests *SomeTest.someSpecificTestMethod
  - ./gradlew test --tests all.in.specific.package*
To run tests and compute coverage reports, run ./gradlew jacocoTestReport. The report is then in build/reports/jacoco/test/html/index.html. (IntelliJ has a good coverage tool that is preferable for development).
We use Travis-CI as our continuous integration provider.
- Before merging any branch make sure that all required tests pass on travis.
- Every travis build will upload the test results to our GATK Google Cloud Storage bucket. A link to the uploaded report will appear at the very bottom of the travis log. Look for the line that says See the test report at. If TestNG itself crashes there will be no report generated.
We use Broad Jenkins for our long-running tests and performance tests.
- To add a performance test (requires Broad-ID), you need to make a "new item" in Jenkins and make it a "copy" instead of a blank project. You need to base it on either the "-spark-" jobs or the other kind of jobs and alter the commandline.
To output stack traces for UserException set the environment variable GATK_STACKTRACE_ON_USER_EXCEPTION=true

Using Git LFS to download and track large test data

We use git-lfs to version and distribute test data that is too large to check into our repository directly. You must install and configure it in order to be able to run our test suite.

After installing git-lfs, run git lfs install
- This adds hooks to your git configuration that will cause git-lfs files to be checked out for you automatically in the future.
To manually retrieve the large test data, run git lfs pull from the root of your GATK git clone.
- The download is several hundred megabytes.
To add a new large file to be tracked by git-lfs, simply:
- Put the new file(s) in src/test/resources/large (or a subdirectory)
- git add the file(s), then git commit -a
- That's it! Do not run git lfs track on the files manually: all files in src/test/resources/large are tracked by git-lfs automatically.

Creating a GATK project in the IntelliJ IDE (last tested with version 2016.2.4):

Ensure that you have gradle and the Java 8 JDK installed
You may need to install the TestNG and Gradle plugins (in preferences)
Clone the GATK repository using git
In IntelliJ, click on "Import Project" in the home screen or go to File -> New... -> Project From Existing Sources...
Select the root directory of your GATK clone, then click on "OK"
Select "Import project from external model", then "Gradle", then click on "Next"
Ensure that "Gradle project" points to the build.gradle file in the root of your GATK clone
Select "Use auto-import" and "Use default gradle wrapper".
Make sure the Gradle JVM points to Java 1.8
Click "Finish"
After downloading project dependencies, IntelliJ should open a new window with your GATK project
Make sure that the Java version is set correctly by going to File -> "Project Structure" -> "Project". Check that the "Project SDK" is set to your Java 1.8 JDK, and "Project language level" to 8 (you may need to add your Java 8 JDK under "Platform Settings" -> SDKs if it isn't there already). Then click "Apply"/"Ok".

Setting up debugging in IntelliJ

Follow the instructions above for creating an IntelliJ project for GATK
Go to Run -> "Edit Configurations", then click "+" and add a new "Application" configuration
Set the name of the new configuration to something like "GATK debug"
For "Main class", enter org.broadinstitute.hellbender.Main
Ensure that "Use classpath of module:" is set to use the "gatk" module's classpath
Enter the arguments for the command you want to debug in "Program Arguments"
Click "Apply"/"Ok"
Set breakpoints, etc., as desired, then select "Run" -> "Debug" -> "GATK debug" to start your debugging session
In future debugging sessions, you can simply adjust the "Program Arguments" in the "GATK debug" configuration as needed

Updating the Intellij project when dependencies change

If there are dependency changes in build.gradle it is necessary to refresh the gradle project. This is easily done with the following steps.

Open the gradle tool window ( "View" -> "Tool Windows" -> "Gradle" )
Click the refresh button in the Gradle tool window. It is in the top left of the gradle view and is represented by two blue arrows.

Setting up profiling using JProfiler

Running JProfiler standalone:
- Build a full GATK4 jar using ./gradlew localJar
- In the "Session Settings" window, select the GATK4 jar, eg. ~/gatk/build/libs/gatk-package-4.alpha-196-gb542813-SNAPSHOT-local.jar for "Main class or executable JAR" and enter the right "Arguments"
- Under "Profiling Settings", select "sampling" as the "Method call recording" method.
Running JProfiler from within IntelliJ:
- JProfiler has great integration with IntelliJ (we're using IntelliJ Ultimate edition) so the setup is trivial.
- Follow the instructions above for creating an IntelliJ project for GATK
- Right click on a test method/class/package and select "Profile"

Uploading Archives to Sonatype (to make them available via maven central)

To upload snapshots to Sonatype you'll need the following:

You must have a registered account on the sonatype JIRA (and be approved as a gatk uploader)
You need to configure several additional properties in your /~.gradle/gradle.properties file
If you want to upload a release instead of a snapshot you will additionally need to have access to the gatk signing key and password

#needed for snapshot upload
sonatypeUsername=<your sonatype username>
sonatypePassword=<your sonatype password>

#needed for signing a release
signing.keyId=<gatk key id>
signing.password=<gatk key password>
signing.secretKeyRingFile=/Users/<username>/.gnupg/secring.gpg

To perform an upload, use

./gradlew uploadArchives

Currently all builds are considered snapshots. The archive name is based off of git describe.

Building GATK4 Docker images

Please see the the Docker README in scripts/docker. This has instructions for the Dockerfile in the root directory.

Releasing GATK4

Please see the How to release GATK4 wiki article for instructions on releasing GATK4.

Generating GATK4 documentation

To generate GATK documentation, run ./gradlew gatkDoc

Generated docs will be in the build/docs/gatkdoc directory.

Using Zenhub to track github issues

We use Zenhub to organize and track github issues.

To add Zenhub to github, go to the Zenhub home page while logged in to github, and click "Add Zenhub to Github"
Zenhub allows the GATK development team to assign time estimates to issues, and to mark issues as Triaged/In Progress/In Review/Blocked/etc.

How to contribute to GATK

(Note: section inspired by, and some text copied from, Apache Parquet)

We welcome all contributions to the GATK project. The contribution can be a issue report or a pull request. If you're not a committer, you will need to make a fork of the gatk repository and issue a pull request from your fork.

To become a committer, you need to make several high-quality code contributions and be approved by the current committers.

For ideas on what to contribute, check issues labeled "Help wanted (Community)". Comment on the issue to indicate you're interested in contibuting code and for sharing your questions and ideas.

To contribute a patch:

Break your work into small, single-purpose patches if possible. It’s much harder to merge in a large change with a lot of disjoint features.
Submit the patch as a GitHub pull request against the master branch. For a tutorial, see the GitHub guides on forking a repo and sending a pull request. If applicable, include the issue number in the pull request name.
Make sure that your code passes all our tests. You can run the tests with ./gradlew test in the root directory.
Add tests for all new code you've written. We prefer unit tests but high quality integration tests that use small amounts of data are acceptable.
Follow the General guidelines for GATK4 developers.

We tend to do fairly close readings of pull requests, and you may get a lot of comments. Some things to consider:

Write tests for all new code.
Document all classes and public methods.
For all public methods, check validity of the arguments and throw IllegalArgumentException if invalid.
Use braces for control constructs, if, for etc.
Make classes, variables, parameters etc final unless there is a strong reason not to.
Give your operators some room. Not a+b but a + b and not foo(int a,int b) but foo(int a, int b).
Generally speaking, stick to the Google Java Style guide

Thank you for getting involved!

Discussions

GATK forum for general discussions on how to use the GATK and support questions.
Issue tracker to report errors and enhancement ideas.
Discussions also take place in GATK pull requests

Authors

The authors list is maintained in the AUTHORS file. See also the Contributors list at github.

License

Licensed under the BSD License. See the LICENSE.txt file.

LauraLP/CtDNATools

GATK 4

Table of Contents

Requirements

Quick Start Guide

Downloading GATK4

Building GATK4

Running GATK4

Passing JVM options to gatk-launch

Running GATK4 with inputs on Google Cloud Storage:

Running GATK4 Spark tools on a Spark cluster:

Running GATK4 Spark tools on Google Cloud Dataproc:

Note on 2bit Reference

Using R to generate plots

Running the CNV workflows

Bash Command-line Tab Completion (BETA)

For GATK Developers

General guidelines for GATK4 developers

Testing GATK

Using Git LFS to download and track large test data

Creating a GATK project in the IntelliJ IDE (last tested with version 2016.2.4):

Setting up debugging in IntelliJ

Updating the Intellij project when dependencies change

Setting up profiling using JProfiler

Uploading Archives to Sonatype (to make them available via maven central)

Building GATK4 Docker images

Releasing GATK4

Generating GATK4 documentation

Using Zenhub to track github issues

Further Reading on Spark

How to contribute to GATK

Discussions

Authors

License