update readmes

Author: sa501428

CONTRIBUTING.md

@@ -1,12 +1,15 @@
-# Contributing to Juicebox and/or Juicebox Assembly Tools
+# Contributing to HiC Tools
 
 :+1::tada: First off, thanks for taking the time to contribute! :tada::+1:
 
-The following is a set of guidelines for contributing to Juicebox and its modules, which are hosted in the [Aiden Lab Repositories](https://github.com/aidenlab) on GitHub. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
+These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a
+pull request.
 
 ## Code of Conduct
 
-This project and everyone participating in it is governed by the [Juicebox Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [[email protected]](mailto:[email protected]).
+This project and everyone participating in it is governed by the [Code of Conduct](CODE_OF_CONDUCT.md). By
+participating, you are expected to uphold this code. Please report unacceptable behavior
+to [[email protected]](mailto:[email protected]).
 
 ## I don't want to read this whole thing I just have a question!!!
 
@@ -16,9 +19,13 @@ While we strongly suggest using the public forum so that the community at large
 
 ## **Did you find a bug?**
 
-* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/aidenlab/Juicebox/issues).
+* **Ensure the bug was not already reported** by searching on GitHub
+  under [Issues](https://github.com/aidenlab/hictools/issues).
 
-* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/aidenlab/juicebox/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample, executable test case, or clear set of instructions** demonstrating the expected behavior that is not occurring.
+* If you're unable to find an open issue addressing the
+  problem, [open a new one](https://github.com/aidenlab/juicebox/issues/new). Be sure to include a **title and clear
+  description**, as much relevant information as possible, and a **code sample, executable test case, or clear set of
+  instructions** demonstrating the expected behavior that is not occurring.
 
 ## **Did you write a patch that fixes a bug?**
 

Juicer.README

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016 Aiden Lab
+Copyright (c) 2022 Rice University, Baylor College of Medicine, Aiden Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

LICENSE

@@ -1,17 +1,21 @@
 --------------
-About Juicebox
+About HiC Tools
 --------------
-Juicebox is visualization software for Hi-C data.  This distribution includes the source code for Juicebox, <a href="https://github.com/theaidenlab/juicer/wiki/Download">Juicer Tools</a>, and <a href="https://aidenlab.org/assembly/">Assembly Tools</a>.  <a href="https://github.com/theaidenlab/juicebox/wiki/Download">Download Juicebox here</a>, or use <a href="https://aidenlab.org/juicebox">Juicebox on the web</a>.  Detailed documentation is available <a href="https://github.com/theaidenlab/juicebox/wiki">on the wiki</a>. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.
+HiC Tools is a software package used to build `.hic` files. This distribution includes the source code for this set of
+tools and builds the latest `v9` `.hic` files.
 
-Juicebox can now be used to visualize and interactively (re)assemble genomes. 
-Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for 
-more details on how to use Juicebox for assembly.
+Previously, this software used to be bundled with Juicer Tools in the Juicebox repo.
 
+HiC Tools was originally created by <a href="https://github.com/jrobinso">Jim Robinson</a>,
+<a href="https://github.com/nchernia">Neva C. Durand</a>, and <a href="http://www.erez.com/">Erez Lieberman Aiden</a>.
+It has been substantially upgraded and improved by <a href="https://github.com/sa501428">Muhammad S Shamim</a>,
+<a href="https://github.com/suhas-rao">Suhas S.P. Rao</a>, and many additional contributors.
 
-Juicebox was created by <a href="https://github.com/jrobinso">Jim Robinson</a>,
-<a href="https://github.com/nchernia">Neva C. Durand</a>, and <a href="http://www.erez.com/">Erez Lieberman Aiden</a>. Past contributors include <a href="https://github.com/imachol">Ido Machol</a>, <a href="https://github.com/zgire">Zulkifl Gire</a>, <a href="https://github.com/mhoeger">Marie Hoeger</a>, <a href="https://github.com/asddf123789">Fanny Huang</a>, <a href="https://github.com/mikeehman">Nam Hee Kim</a>, <a href="https://github.com/nguyenkvi">Vi Nguyen</a>, <a href="https://github.com/bluejay9676">Jay Ryu</a>, <a href="https://github.com/musianat">Nathaniel T. Musial</a>, and <a href="https://github.com/ranganmostofa11">Ragib Mostofa</a>.
+**If you use HiC Tools in your research, please cite:
+Neva C. Durand, Muhammad S. Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman
+Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments."
+Cell Systems 3(1), 2016.**
 
-Ongoing development work is carried out by <a href="https://github.com/sa501428">Muhammad Saad Shamim</a>, <a href="https://github.com/nchernia">Neva C. Durand</a>, and <a href="https://github.com/dudcha">Olga Dudchenko</a>.
 
 --------------
 Questions?
@@ -29,111 +33,29 @@ To set up in IDEA, have the Java SDK installed
 then you'll point to it (IntelliJ has lots of documentation on this sort of thing).
 
 * Then go to `VCS` -> `checkout from version control`.
-* You'll need to do is be sure `*.sizes` is included as a file to be copied over to the class files.
-Set this up via IntelliJ `Preferences` -> `Compiler`. Add `?*.sizes` to the list of `Resource Patterns`.
-* While there, also go to `Java Compiler` and put this into additional command line options: `-Xlint:all -target 1.7`
-The former turns on all warnings, the latter gives some flexibility since some people haven't updated Java to 1.8 yet.
 * Then go to `Run` -> `Edit Configurations`.
 * With the `+` sign, add `Application`.
-* You'll create two of these, one for the GUI (call it Juicebox GUI or whatever you want, really) and one for the CLT.
+* You'll create one of these for HiC Tools.
 * Set the main class by clicking the little `...` button next to the text box for main class
-
-        MainWindow.java is the main method class for the visualization/GUI portion of the software.
-        HiCTools.java is the main method class for the analysis/CLT portion.
-
-* For the GUI under VM Options:
-
-        -Xmx2000m
-        -Djnlp.loadMenu="https://hicfiles.tc4ga.com/juicebox.properties"
-
-* For the CLT use
-
-        -Xmx2000m
-
-* Note that the `Xmx2000m` flag sets the maximum memory heap size to 2GB.
-Depending on your computer you might want more or less.
-Some tools will break if there's not enough memory and the file is too large,
-but don't worry about that for development; 2GB should be fine.
+* HiCTools.java is the main method class.
+* Under VM Options, set `-Xmx2000m`
+* The `Xmx2000m` flag sets the maximum memory heap size to 2GB. Depending on your computer you might want more or less.
+  Some tools will break if there's not enough memory and the file is too large, but don't worry about that for
+  development; 2GB should be fine.
 * One last note: be sure to `Commit and Push` when you commit files, it's hidden in the dropdown menu button in the
-commit window.
+  commit window.
 
 ----------------------------------
 Hardware and Software Requirements
 ----------------------------------
 The minimum software requirement to run Juicebox is a working Java installation
-(version > 1.6) on Windows, Linux, and Mac OSX.  We recommend using the latest
-Java version available, but please do not use the Java Beta Version. Minimum
-system requirements for running Java can be found at
-https://java.com/en/download/help/sysreq.xml. To download and install the latest
-Java Runtime Environment (JRE), please go to https://www.java.com/download.
-
-We recommend having at least 2GB free RAM for the best user experience with
-Juicebox.
-
-To launch the Juicebox application from command line, type
-  java -Xms512m -Xmx2048m -jar Juicebox.jar
-
-Note: the -Xms512m flag sets the minimum memory heap size at 512 megabytes, and
-the -Xmx2048m flag sets the maximum size at 2048 megabytes (2 gigabytes). These
-values may be adjusted as appropriate for your machine.
+(version > 1.8) on Windows, Linux, and Mac OSX. We recommend using the latest Java version available, but please do not
+use the Java Beta Version. Minimum system requirements for running Java can be found at
+https://java.com/en/download/help/sysreq.xml. To download and install the latest Java Runtime Environment (JRE), please
+go to https://www.java.com/download.
 
 -------------
 Documentation
 -------------
-We have extensive documentation for how to use Juicebox at
-https://github.com/theaidenlab/juicebox/wiki including a video, a Quick Start Guide, and a
-detailed tutorial.
-
-For using Juicebox to assemble genomes see https://www.aidenlab.org/assembly/.
-
-------------------------
-Command Line Tools Usage
-------------------------
-
-See the documentation at https://github.com/theaidenlab/juicer/wiki for information
-on how to use the Juicer tools.
-
---------------------------------
-Compiling Jars from Source Files
---------------------------------
-1. You should have Java 1.8 JDK and Apache Ant installed on your system. See
-   below for more information.
-2. Go to the folder containing the Juicebox source files and edit the
-   juicebox.properties file with the proper Java JDK Address.
-3. Open the command line, navigate to the folder containing the build.xml file
-   and type
-     ant
-   The process should take no more than a minute to build on most machines.
-4. The jars are written to the directory out/.  You can change this by editing
-   the build.xml file.
-
-* Installing Java 1.8 JDK
-
-For Windows/Mac/Linux, the Java 1.8 JDK can be installed from here:
-https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
-(Alternative) For Ubuntu/LinuxMint
-https://tecadmin.net/install-oracle-java-8-jdk-8-ubuntu-via-ppa/
-
-* Installing Apache Ant
-Mac
-  Ant should be installed on most Macs. To verify installation via the command
-  prompt, type
-    ant -version
-  If Ant is not on your Mac, install it via homebrew. At the command prompt, type
-    brew update
-    brew install ant
-  You may need to install Homebrew (https://brew.sh/) on your machine
-  See the following Stackoverflow post for more details:
-  https://stackoverflow.com/questions/3222804/how-can-i-install-apache-ant-on-mac-os-x
-
-Windows
-  Installing Ant requires some minor changes to your system environment. Follow
-  the instructions in this article:
-  https://www.nczonline.net/blog/2012/04/12/how-to-install-apache-ant-on-windows/
-
-Linux
-  In the command prompt, type
-    sudo apt-get install ant
-  or
-    sudo yum install ant
-  depending on your package installer
+We have extensive documentation for how to use HiC Tools at
+https://github.com/aidenlab/juicer/wiki.