Resolve merge conflicts

.gitattributes

@@ -0,0 +1,2 @@
+testdata/picard/reference/test_windows_line_endings.fasta eol=crlf
+

.github/ISSUE_TEMPLATE.md

@@ -1,3 +1,7 @@
+## ***This issue tracker is for bug reports only. Before opening a new issue here, please make a post on our [support forum](https://gatk.broadinstitute.org/hc/en-us/community/topics) so that our support team can look at your issue and determine whether it needs to be escalated into a bug report.***
+
+----
+
 ### Instructions
 
 - Use a **concise** yet **descriptive** title;
@@ -49,4 +53,4 @@ _Tool name(s), parameters?_
 ### Description 
 _Describe what needs to be added or modified._
 
-----
+----

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,7 @@ Never delete this, it is our record that procedure was followed. If you find tha
 #### Content
 - [ ] Added or modified tests to cover changes and any new functionality
 - [ ] Edited the README / documentation (if applicable)
-- [ ] All tests passing on Travis
+- [ ] All tests passing on github actions
 
 #### Review
 - [ ] Final thumbs-up from reviewer

.github/workflows/cloud_tests.yml

@@ -0,0 +1,93 @@
+name: Cloud Tests
+on:
+  push:
+    branches:
+      - 'master'
+  pull_request:
+  workflow_dispatch:
+
+env:
+  PICARD_TEST_INPUTS: gs://hellbender/test/resources/
+  PICARD_TEST_STAGING: gs://hellbender-test-logs/staging/
+  PICARD_TEST_LOGS: /hellbender-test-logs/build_reports/
+  PICARD_TEST_PROJECT: broad-dsde-dev
+
+jobs:
+  ## This workaround is necessary since there is no equivalent to the old TRAVIS_SECURE_ENVIRONMENT variable that indicated
+  ## if a run was privileged and had secrets. Since the GCP credentials are necessary for all tests in order to upload their,
+  ## results that makes them a reasonable proxy for testing the credentials of this entire execution. https://github.com/actions/runner/issues/520
+  check-secrets:
+    name: check if the environment has privileges
+    outputs:
+      google-credentials: ${{ steps.google-credentials.outputs.defined }}
+    runs-on: ubuntu-latest
+    steps:
+      - id: google-credentials
+        env:
+          GCP_CREDENTIALS: ${{ secrets.GCP_CREDENTIALS }}
+        if: "${{ env.GCP_CREDENTIALS != '' }}"
+        run: echo defined=true >> $GITHUB_OUTPUT
+
+  test:
+    runs-on: ubuntu-latest
+    needs: check-secrets
+    strategy:
+      matrix:
+        java: [ 17 ]
+        run_barclay_tests: [true, false]
+        experimental: [ false ]
+      fail-fast: false
+    continue-on-error: ${{ matrix.experimental }}
+    name: Java ${{ matrix.Java }}, Barclay=${{ matrix.run_barclay_tests}} cloud tests
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: 'Set up java ${{ matrix.Java }}'
+        uses: actions/setup-java@v3
+        with:
+          java-version: ${{ matrix.Java }}
+          distribution: 'temurin'
+          cache: gradle
+
+      - name: 'Compile with Gradle'
+        run: |
+          ./gradlew compileJava 
+          ./gradlew installDist
+
+      #Google Cloud stuff
+      - id: 'gcloud-auth'
+        if: needs.check-secrets.outputs.google-credentials == 'true'
+        uses: google-github-actions/auth@v0
+        with:
+          credentials_json: ${{ secrets.GCP_CREDENTIALS }}
+          project_id: ${{ env.PICARD_TEST_PROJECT }}
+          create_credentials_file: true
+
+      - name: 'Set up Cloud SDK'
+        if: needs.check-secrets.outputs.google-credentials == 'true'
+        uses: google-github-actions/setup-gcloud@v2
+
+      - name: compile test code
+        if: needs.check-secrets.outputs.google-credentials == 'true'
+        run: ./gradlew compileTestJava
+
+      - name: Run tests
+        if: needs.check-secrets.outputs.google-credentials == 'true'
+        env:
+          TEST_TYPE: cloud
+        run: |
+          if [[ ${{matrix.run_barclay_tests}} == true ]]; then
+            echo "Running tests using the Barclay command line parser."
+            ./gradlew barclayTest
+          else
+            echo "Running tests using the legacy Picard command line parser."
+            ./gradlew jacocoTestReport
+          fi
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: cloud-test-results-${{ matrix.Java }}-barclay-${{ matrix.run_barclay_tests}}
+          path: build/reports/tests

.github/workflows/tests.yml

@@ -0,0 +1,59 @@
+# This is a github actions workflow which runs picard tests
+
+name: Build and Test
+on:
+  push:
+    branches: [master]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ 17 ]
+        experimental: [false]
+        run_barclay_tests: [true, false]
+      fail-fast: false
+    continue-on-error: ${{ matrix.experimental }}
+    name: Java ${{ matrix.Java }}, Barclay=${{ matrix.run_barclay_tests}} tests
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up java ${{ matrix.Java }}
+        uses: actions/setup-java@v3
+        with:
+          java-version: ${{ matrix.Java }}
+          distribution: 'temurin'
+          cache: gradle
+      - name: "set up R"
+        run: |
+          wget -q -O - https://dl.google.com/linux/linux_signing_key.pub | sudo apt-key add -
+          sudo apt-get -qq update
+          sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf
+      - name: Grant execute permission for gradlew
+        run: chmod +x gradlew
+      - name: Compile with Gradle
+        run: ./gradlew compileJava
+      - name: Run tests
+        run: |
+          if [[ ${{matrix.run_barclay_tests}} == true ]]; then
+            echo "Running tests using the Barclay command line parser."
+            ./gradlew barclayTest
+          else
+            echo "Running tests using the legacy Picard command line parser."
+            ./gradlew jacocoTestReport
+          fi
+      - name: "Build the jar and run a commandline test for sanity checking"
+        run: |
+          ./gradlew currentJar
+          java -jar build/libs/picard.jar MarkDuplicates -I testdata/picard/sam/aligned_queryname_sorted.bam -O out.bam --METRICS_FILE out.metrics
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: test-results-${{ matrix.Java }}-barclay-${{ matrix.run_barclay_tests}}
+          path: build/reports/tests
+
+
+

.github/workflows/trivy.yml

@@ -0,0 +1,12 @@
+name: dsp-appsec-trivy
+on: [pull_request]
+
+jobs:
+  appsec-trivy:
+    # Parse Dockerfile and build, scan image if a "blessed" base image is not used
+    name: DSP AppSec Trivy check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: broadinstitute/dsp-appsec-trivy-action@v1

.gitignore

@@ -15,3 +15,10 @@ report
 jacoco.data
 .gradle
 build
+*.swp
+.vscode
+# OSX file system stuff
+.DS_STORE
+
+# Jenv file to set directory java version
+.java-version

Dockerfile

@@ -1,35 +1,37 @@
-FROM openjdk:8 
-MAINTAINER Broad Institute DSDE <[email protected]>
+ARG BASE_DOCKER=eclipse-temurin:17-jdk
+ARG release=false
 
-ARG build_command=shadowJar
-ARG jar_name=picard.jar
+FROM ${BASE_DOCKER} as build
+LABEL stage=buildStage
 
-# Install ant, git for building
+# Install git for building
 RUN apt-get update && \
-    apt-get --no-install-recommends install -y --force-yes \
-        git \
-        r-base \
-        ant && \
-    apt-get clean autoclean && \
-    apt-get autoremove -y
+    apt-get --no-install-recommends install -y \
+        git
 
 # Assumes Dockerfile lives in root of the git repo. Pull source files into container
 COPY / /usr/picard/
 WORKDIR /usr/picard
 
-# Build the distribution jar, clean up everything else
-RUN ./gradlew ${build_command} && \
-    mv build/libs/${jar_name} picard.jar && \
-    mv src/main/resources/picard/docker_helper.sh docker_helper.sh && \
-    ./gradlew clean && \
-    rm -rf src && \
-    rm -rf gradle && \
-    rm -rf .git && \
-    rm gradlew && \
-    rm build.gradle
+# download gradle then build
+RUN ./gradlew -Drelease=${release} \
+   clean \
+   printVersion \
+   shadowJar
+
+FROM ${BASE_DOCKER} as final
+MAINTAINER Broad Institute DSDE <[email protected]>
+
+# Install R
+RUN apt-get update && \
+    apt-get --no-install-recommends install -y \
+        r-base &&\
+    apt-get clean autoclean && \
+    apt-get autoremove -y
+
+RUN mkdir /usr/picard/
+
+COPY --from=build /usr/picard/build/libs/picard.jar /usr/picard/
 
 RUN mkdir /usr/working
 WORKDIR /usr/working
-
-ENTRYPOINT ["/usr/picard/docker_helper.sh"]
-CMD [""]

LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017 Broad Institute
+Copyright (c) 2017-2021 Broad Institute
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal