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Merge branch 'master' into galaxy-wrappers-corepipeline
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‎.classpath‎

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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" path="src"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
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<classpathentry kind="lib" path="lib/jcommon-1.0.21.jar"/>
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<classpathentry kind="lib" path="lib/jfreechart-1.0.17.jar"/>
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<classpathentry kind="lib" path="lib/jfreesvg-3.0.jar"/>
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<classpathentry kind="lib" path="lib/picard.jar"/>
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<classpathentry kind="output" path="bin"/>
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</classpath>
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<classpathentry kind="src" output="bin/main" path="src/main/resources">
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<attributes>
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<attribute name="gradle_scope" value="main"/>
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<attribute name="gradle_used_by_scope" value="main,test"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="bin/test" path="src/test/java">
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<attributes>
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<attribute name="gradle_scope" value="test"/>
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<attribute name="gradle_used_by_scope" value="test"/>
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<attribute name="test" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="bin/test" path="src/test/resources">
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<attributes>
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<attribute name="gradle_scope" value="test"/>
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<attribute name="gradle_used_by_scope" value="test"/>
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<attribute name="test" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="bin/main" path="src/main/java">
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<attributes>
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<attribute name="gradle_scope" value="main"/>
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<attribute name="gradle_used_by_scope" value="main,test"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
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<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
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<classpathentry kind="output" path="bin/default"/>
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</classpath>

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Report bugs so we can fix them
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title: ''
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labels: bug
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assignees: ''
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---
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Please complete the following information:
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#### Describe the bug
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A clear and concise description of what the bug is.
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#### Environment:
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- ScriptManager version =
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(run `java -jar /path/to/scriptmanager.jar --version`)
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- Java Version =
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(run `java --version`)
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- OS =
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(run `uname -sr` on Linux/Mac OS or ` wmic os get Caption, Version` on Windows)
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- machine architecture =
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(run `uname -m` on Linux/Mac OS or ` wmic os get OSArchitecture` on Windows)
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#### To Reproduce
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Are you running ScriptManager from the graphical interface (GUI) or the command line (CLI)?
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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#### Expected behavior
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A clear and concise description of what you expected to happen.
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#### Screenshots
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If applicable, add screenshots to help explain your problem.
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#### Additional context
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/new-tool.md‎

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---
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name: New Tool
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about: Use this template's checklist for brand new tools
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title: ''
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labels: New Tool
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assignees: ''
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---
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## Describe tool
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... Blah blah blah blah...
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## Checklist
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New tools should be written on branches off `dev`. A pull request to the `dev` branch can then be submitted and a reviewer will review the code and accept the merge.
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- [ ] Write tests
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- [ ] Write tool (list changed files)
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- [ ] `objects.ToolDescriptions.java`
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- [ ] `scripts.MyTool.java`
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- [ ] `cli.MyToolCLI.java`
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- [ ] `window_interface.MyToolWindow.java`
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- [ ] `window_interface.MyToolOutput.java`
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- [ ] `main.ScriptManagerGUI.java`
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- [ ] `main.ScriptManager.java`
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- [ ] Add logging support
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- [ ] Update documentation (docusaurus)
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- [ ] Write Galaxy wrapper
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Then you can pull your changes into master! 🎉

‎.github/PULL_REQUEST_TEMPLATE/version-increment.md‎

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---
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name: Version Increment
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about: Use this template's checklist to version increment
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---
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The [Release Roadmap](https://github.com/orgs/CEGRcode/projects/9) on Github organizes issue tickets and creates a projection of which issues should be addressed for each release. This helps when writing up the release notes/change log, tagging all the appropriate issues, as well as visually tracking what tasks are left to do in each release. When we are ready for a release, the following checklist should be followed to ensure that we update everything together without missing anything.
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### Check [Release Roadmap]((https://github.com/orgs/CEGRcode/projects/9))
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- [ ] Make sure all issues are closed and pulled into dev
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- [ ] Update roadmap so next version is first to display
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### [Docusaurus updates](https://github.com/CEGRcode/scriptmanager-docs)
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- [ ] Make sure new tools have their own pages that thoroughly describe what they do
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- [ ] Affected tools have been updated accordingly (check logs for list of tools)
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- [ ] Make sure last updated timestamps are appropriate/correct
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- [ ] Increment version across docs
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- [ ] Update Download links for latest version on the Getting Started page
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### Testing
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- [ ] Ideally some degree of user testing on the development version has been performed (ask the bench scientists).
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- [ ] Make sure latest [Github Actions build](https://github.com/CEGRcode/scriptmanager/actions/workflows/gradle.yml) ran successfully
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- [ ] Any CI tests that exist should be run (`gradlew test`)
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### Release commit
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- [ ] `build.gradle`
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- [ ] Increment version (`version = ____`) and strip dev from JAR filename
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- [ ] `src/objects/ToolDescriptions.java`
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- [ ] Increment ScriptManager version constant (used by all CLI tools and GUI JFrame title for versioning)
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### Github Release/version tag
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- [ ] Commit & pull request, review into master
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- [ ] Create version release & add version tag to the commit id
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- [ ] Compile JAR and save with source tar archive on release page
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- [ ] Write up summary for the version tag commit including change log that links to resolved/relevant issue tickets (refer to Release Roadmap)
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### Switch naming back to dev
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- [ ] `build.gradle` file should switch naming JAR to use dev
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- [ ] `src/objects/ToolDescriptions.java` file should switch naming JAR to use dev

‎.github/workflows/gradle.yml‎

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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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# This workflow will build a Java project with Gradle and cache/restore any dependencies to improve the workflow execution time
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-gradle
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# Modified to matrix test across three OS and two Temurin distributions of Java - two LTS versions (11 and 17)
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name: Java CI with Gradle
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on:
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push:
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branches: [ "master" ]
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pull_request:
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branches: [ "master", "dev" ]
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permissions:
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contents: read
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jobs:
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build:
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name: Build on node ${{ matrix.java_version }} and ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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java_version: ['11', '17']
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os: [ ubuntu-latest, windows-latest, macOS-latest ]
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steps:
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- uses: actions/checkout@v3
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- name: Set up JDK ${{ matrix.java_version }} on ${{ matrix.os }}
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uses: actions/setup-java@v3
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with:
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java-version: ${{ matrix.java_version }}
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distribution: 'temurin'
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- name: Build with Gradle
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uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
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with:
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arguments: build

‎.gitignore‎

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**/.DS_Store
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/bin
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/.gradle/
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/build/
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.metadata
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.idea

‎.project‎

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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
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<arguments>
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</arguments>
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</buildCommand>

‎.settings/org.eclipse.buildship.core.prefs‎

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connection.project.dir=
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eclipse.preferences.version=1
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eclipse.preferences.version=1

‎README.md‎

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# scriptmanager
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### GUI pipeline containing useful NGS analysis scripts.
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# ScriptManager
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Scripts are generically categorized within semi-descriptive tabs and are designed to be run in parallel with each other and themselves.
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ScriptManager was built to be a lightweight and easy to use genomics analysis tool for novice bioinformaticians. It includes both a graphical interface for easy navigation of inputs and options while also supporting a command line interface for automation and integration with workflow managers like Galaxy. We describe here how a user unfamiliar with the command line can leverage national supercomputing resources using a graphical desktop interface like Open OnDemand to perform their analyses and generate publication quality figures for their research. Widespread adoption of this tool in the genomics community would lower technical barriers to accessing supercomputing resources and allow biochemists to prototype their own workflows that can be integrated into large scale production pipelines. Source code and precompiled binaries available at https://github.com/CEGRcode/scriptmanager.
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### [:house: ScriptManager Website Homepage :house:](https://pughlab.mbg.cornell.edu/scriptmanager-docs/)
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### Tutorial to using basic plotting capabilities of ScriptManager
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Open **ScriptManager-Tutorial.docx** available in root directory
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## Documentation Quick-links
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* [Getting Started](https://pughlab.mbg.cornell.edu/scriptmanager-docs/)
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* [Full list of scripts available](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/References/tool-index) - Scripts are generically categorized within semi-descriptive tabs and are designed to be run in parallel with each other and themselves.
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## Build Instructions
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(after cloning this repo):
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```
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$ cd scriptmanager
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$ ./gradlew build
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```
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## Tutorials
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* [ChIP-exo Tutorial](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tutorials/chipexo-tutorial)
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* [Four-color Sequence Plot Tutoral](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tutorials/genomic-features-tutorial)
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The compiled JAR file will be output into the `build/libs` directory.
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## Pugh Lab Favorite Tools
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:star: [Tag Pileup](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tools/read-analysis/tag-pileup)
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:star: [Expand BED](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tools/coordinate-manipulation/expand-bed)
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:star: [Align BED to Reference](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tools/peak-analysis/peak-align-ref)
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:star: [Aggregate Data](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tools/read-analysis/aggregate-data)
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:star: [Scaling Factor](https://pughlab.mbg.cornell.edu/scriptmanager-docs/docs/Tools/read-analysis/scaling-factor) :star:
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## Running ScriptManager
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## Citing Us
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If you use ScriptManager in your work, you can use the Lang et al (2022) publication or use ScriptManager's unique [RRID:SCR_021797](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_021797/resolver?q=SCR_021797%2A&l=SCR_021797%2A&i=rrid:scr_021797).
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To run the GUI verson of ScriptManager, you can double click the compiled JAR file or run the followinug command in the terminal
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```
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$ java -jar /path/to/jarfile
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```
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Running the CLI version of ScriptManager is similar to running the GUI. To view the list of command options, use the `-h` flag.
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```
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$ java -jar /path/to/jarfile -h
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```
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**Example:**
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```
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$ java -jar /path/to/jarfile coordinate-manipulation bed-to-gff BEDFILE.bed -o OUTPUT.gff
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```
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## Current scripts available (210106):
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**BAM Statistics:**
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-BAM Statistics
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-Paired-End Statistics
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-BAM Genome Correlation
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**BAM Manipulation:**
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-BAM-BAI Indexer
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-BAM File Sorter
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-BAM Remove Duplicates
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-BAM Replicate Merge
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-Filter for PIP-seq
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**BAM Format Converter:**
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-BAM to scIDX
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-BAM to GFF
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-BAM to BED
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-BAM to bedGraph
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**File Utilities:**
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-MD5 Checksum
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**Peak Calling:**
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-Genetrack - still highly unstable
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**Peak Analysis:**
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-Align BED to Reference
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-Filter BED by Proximity
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-Genomic Coordinate Tile
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-Generate Random Coordinate
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-Signal Duplication
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**Coordinate File Manipulation:**
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-Expand BED/GFF File
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-Convert BED/GFF to GFF/BED
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-Sort BED/GFF by CDT
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**Sequence Read Analysis:**
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-Tag Pileup
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-Calculate Scaling Factor
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-Scale Matrix Data
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-Aggregate Data
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**DNA Sequence Analysis:**
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-FASTA from BED
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-Randomize FASTA
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-Search Motif in FASTA
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-DNA Shape from BED
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-DNA Shape from FASTA
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**Figure Generation:**
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-Heatmap
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-Merge Heatmaps
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-4Color Sequence Plot
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* Lang OW, Pugh BF, Lai WKM. ScriptManager: an interactive platform for reducing barriers to genomic analysis. PEARC'22. 2022 Jul. [doi: 10.1145/3491418.3535161](https://dl.acm.org/doi/abs/10.1145/3491418.3535161).

‎ScriptManager-Tutorial.docx‎

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