initial commit

.gitignore

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+
+# Vault-generated configuration files
+**/application.yml
+**/orsp-client.json
+
+*~
+.DS_Store
+/target
+/classes
+*.war
+*.log
+*.ipr
+*.pub
+.classpath
+.project
+.slcache
+/migration
+
+### Gradle template
+.gradle
+build/
+
+# Ignore Gradle GUI config
+gradle-app.setting
+
+# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
+!gradle-wrapper.jar
+
+# Cache of project
+.gradletasknamecache
+
+# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
+# gradle/wrapper/gradle-wrapper.properties
+### Grails template
+# .gitignore for Grails 1.2 and 1.3
+# Although this should work for most versions of grails, it is
+# suggested that you use the "grails integrate-with --git" command
+# to generate your .gitignore file.
+
+# web application files
+/web-app/WEB-INF/classes
+
+# default HSQL database files for production mode
+/prodDb.*
+
+# general HSQL database files
+*Db.properties
+*Db.script
+
+# logs
+/stacktrace.log
+/test/reports
+/logs
+
+# project release file
+/*.war
+
+# plugin release files
+/*.zip
+/plugin.xml
+
+# older plugin install locations
+/plugins
+/web-app/plugins
+
+# "temporary" build files
+### JetBrains template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+## File-based project format:
+*.iws
+
+# IntelliJ
+**.iml
+.idea
+/out/
+/buildSrc/out/
+/..bfg-report
+.idea_modules/

LICENSE.txt

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+Copyright (c) 2014, Broad Institute, Inc.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name Broad Institute, Inc. nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE

hooks/README.md

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+# git secrets
+* If you have not done so already please run `brew install git-secrets`
+* To ensure git secrets is run please copy or link this directory to .git/hooks/ locally.
+* This is done for you if you use the rsync script to spin sam up locally.
+* For more information see: https://broadinstitute.atlassian.net/wiki/spaces/GAWB/pages/136445956/Git+Secrets+SHHHHH

hooks/apply-git-secrets.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+
+{ which git-secrets; } || {
+  echo 'git-secrets required and not found. See README for installation instructions.'
+  echo
+  exit 1
+}
+
+{
+  git config --remove-section secrets 2>/dev/null
+} || {
+  :
+}
+git secrets --add 'private_key'
+git secrets --add 'private_key_id'
+git secrets --add --allowed --literal "git secrets --add 'private_key'"
+git secrets --add --allowed --literal "git secrets --add 'private_key_id'"

hooks/commit-msg

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+
+./.git/hooks/apply-git-secrets.sh
+
+git secrets --commit_msg_hook -- "$@"

hooks/pre-commit

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+
+./.git/hooks/apply-git-secrets.sh
+
+git secrets --pre_commit_hook -- "$@"
+
+CURRENT_BRANCH=`git rev-parse --abbrev-ref HEAD`
+if [ "$CURRENT_BRANCH" = "master" ]
+then
+  echo Current branch is master, aborting commit.
+  echo Please commit to a working branch and push it to GitHub for review/merge.
+  exit 1
+fi

hooks/prepare-commit-msg

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+
+./.git/hooks/apply-git-secrets.sh
+git secrets --prepare_commit_msg_hook -- "$@"