Stable release -- Updated to MacOS Big Sur

The full application install instructions are found on the project WIKI site. On Mac OSX, the brew package for RNAStructViz is installed by running:

$ brew tap gtDMMB/homebrew-core
$ brew install gtDMMB/core/rnastructviz

To reinstall the package from a previous release, run the following:

$ brew update
$ brew reinstall --verbose gtDMMB/core/RNAStructViz

Now run the application at your terminal by typing RNAStructViz. Refer to the first-run instructions for pointers on how to configure RNAStructViz the first time you run it.

Testing release of RNAStructViz

The full application install instructions are found on the project WIKI site. On Mac OSX, the brew package for RNAStructViz is installed by running:

$ brew install gtDMMB/core/rnastructviz

To reinstall the package from a previous release, run the following:

$ brew update
$ brew reinstall gtDMMB/core/rnastructviz

Now run the application at your terminal by typing RNAStructViz. Refer to the first-run instructions for pointers on how to configure RNAStructViz the first time you run it.

Testing release of several new requested features

New features added to this release

New features added to this release include the following:

1. Updated the default folder naming procedures so we no longer rely on the file names being in the same (previously expected) format as those in our sample CT files folder.
2. New labeling of the 5'/3' strand start/end positions with arrows indicating position (as in standard biology contexts) added to the program. See the original feature request (issue #18) and the implementation result in the screenshot below.
3. Tick marks and base pair labels indicating relative positions of base pair index numbers from the CT file specs are now drawn around the Diagram Window arc diagrams (see screenshot below). See the discussion for this feature request here (issue #27).
4. Clicking <CTRL+G> after selecting a zoom area in the Diagram Window will now take the user to the relevant position in the open CT viewer window (if one for that structure is already open). See the feature request here (issue #28).
5. Beta testing a radial layout viewer.

New screenshots of the application

DiagramWindow screenshot

Main window screenshot featuring updated folder name defaults

Install notes

For a complete list of installation procedures on all of our supported platforms, please see the documentation on our project WIKI site.

Mac-specific install notes

On a Mac, the instructions typical for a Homebrew install are as follows:

# -- New brew install from source (compiler=gcc): --
$ brew install --build-from-source gtDMMB/core/RNAStructViz
# -- OR New brew install from source (compiler=clang++): --
$ brew install --with-clang --build-from-source gtDMMB/core/RNAStructViz
# -- OR to install a binary bottle (if one is available): --
$ brew install gtDMMB/core/RNAStructViz

Optional installation procedure (help us to maintain binaries for more Mac platform releases!)

If you would like to do us one better, and prepare a binary bottle of the application which other users can install directly, please send the output of the last command to the developers:

$ brew install --build-bottle gtDMMB/core/RNAStructViz
$ brew bottle gtDMMB/core/RNAStructViz

New folder and subfolder naming schemes

Updates to previous releases

The key differences in functionality between this and the previous v1.3.2-production release previously issued on this site are additions to the built-in CT viewer functionality. In particular, given a specific CT file loaded in the Folder (SUb)Window on the right-hand-side of the main application window, we now have the options to:

1. Export the CT file format to both DOT (aka Dot Bracket / DB) and FASTA (plaintext / ascii) file formats;
2. View the (loosely-grouped) raw ACGU sequence (i.e., without the implied pairings) in an initial subwindow which is now concurrently displayed with the CT format viewer that was present in the prior releases;
3. Continue to view the CT file pairings as they have been displayed in the past few relevant releases.

A screenshot of the visual differences in form factor and functionality is shown for reference below:

Install notes

I will be updating the MacOS Homebrew packages to reflect the new source code revisions shortly (And, done: ✔️). As always, for user documentation on all supported methods of installation procedure, be sure to reference the most recent pages on our project WIKI site.

NOTE THAT THE INCLUDED BINARY DEB PACKAGE INSTALLATION METHOD IS ABSOLUTELY UNSUPPORTED FOR USERS (DEVELOPERS ONLY)!

Hints to those who brave an unsuccessful install using this method include: 1) a from-source install (e.g., NOT the latest Debian package) for FLTK v1.4.x is needed on the system in question; and 2) the package does not install all of the necessary dependencies to get this method of binary distribution up and running on most untouched systems. However, it SHOULD work if you have completed a previous (recent-ish) install of RNAStructViz from source on the Debian variant Linux box you are working with. Additional hints as to what key packages are required before installing via the linked .deb package are suggested by reading this from-source install document for Linux users.

Complete production-ready version of RNAStructViz to accompany the Bioinformatics application note submission

v1.3.2-production

New minor version: v1.3.2-production release

Finalized Winter 2018 Semester Release

Release Codename: PRE-MAXIE-COMPS-2019

Install notes (quick reference):

To install RNAStructViz on Mac OSX (non-from-source install) run the following Homebrew command:

$ brew install --build-from-source gtDMMB/core/RNAStructViz

For documentation on from-source installs, and installs on other Unix-based platforms we support, consult this document. Once you have the application installed (and RNAStructViz in your current PATH), you can verify that you're running the latest intended revision of the software by running the following:

$ RNAStructViz --about
==== RNAStructViz v1.2-beta -- CT File Viewer and Structure Comparison Tool ====

ABOUT THIS APPLICATION:
   >> User Manual: https://github.com/gtDMMB/RNAStructViz/wiki
   >> Git Revision: 626d5f2246d1 (626d5f2246d108d464753baaaf7c4f495a3fbef3) [heads/master-168-ga05a11]
   >> Revision Date: Wed Nov 28 16:19:16 2018 -0500
   >> FLTK Library Version: 1.4.0 (API #10400)
   >> Compile-Time FLTK-Config: /home/maxie/RNA-projects/RNAStructViz/src/fltk-config
   >> Cairo Library Version: 1.15.10
   >> Target Platform: Linux (4.15.0-20-generic) [x86_64] @ penguinboxhp
   >> Local Build Time: Wed 28 Nov 2018 04:21:44 PM EST

BUG REPORT INFORMATION:
**Please include a screenshot along with this information in any bug report you submit. New issues with the application can be submitted at https://github.com/gtDMMB/RNAStructViz/issues.**

The output above may not match your results exactly, but the information concerning the application version string and GitHub commit SHA strings (long and shortened hexadecimal strings) are what to check for here.

If you already installed from source, please note that THIS RELEASE is currently the latest stable source for the application. The most recent snapshot of the with-cairo branch should be considered experimental in that occasionally, as development on new features naturally progresses untested bugs may creep in and lead to errors in your user experience. If in doubt, you can check for newer releases at this permanent link.

Recent revision information:

New versions of the software.

Note that these procedures will install from the source code base for what is currently the with-cairo branch of our RNAStructViz software. This branch features a number of improvements and bug fixes from what appears (currently and historically) in the multi-year-old master branch of the software. These updated features include: higher resolution and sharper image quality in the produced arc diagrams using integrated the Cairo drawing library, ability to output the plotted arc diagrams directly to PNG (without the need for intermediate screenshots), aesthetic improvements to the general UI, configuration options and a history of the user's preferences for settings like image save paths and CT file browse paths, as well as miscellaneous bug fixes and patches.

If you have previously downloaded RNAStructViz, or had past issues running this software, PLEASE RE-INSTALL with the more recent branch source!

Credit where it is due.

While the previous revision is a generally good code base, many years passing has led to things like compiler default settings (auto setting of pointer variables to NULL by g++, for example, no longer being default on some Linux distros) changing which then resulted in gradual bug creep into the code. This release has been more thoroughly tested and reviewed by our research team, with special attention by Anna Kirkpatrick, Maxie D. Schmidt, and generous donations of Mac book CPU cycles by Iris Yoon, than the previous revisions and (unofficial) releases of RNAStructViz. Additionally, the grant support of Christine Heitsch has allowed several graduate students to focus on this project over the past months concluding the Fall 2018 school year. The net-net of this attention to the application is an overall improved, more feature rich, and more user friendly experience with the program.

Tentative screenshots and examples featuring the new UI and its features:

Main window (default theme).

Diagrams window (featuring the new Cairo rendering support).

Sample PNG output of the diagrams.

Statistics window.

Configuration settings.

Latest release (With-Cairo Branch) for Homebrew Mac OSX installs

With the exception of Anna's themes, this is the tentative finalized release we will be testing and optimizing for the application note. This release is created for access by our Homebrew installer on Mac OSX, which can be run by executing the following commands at your terminal:

$ brew install --build-from-source gtDMMB/core/RNAStructViz

For all other install procedures (i.e., besides brew on Mac OSX), see this user documentation for details of installing RNAStructViz from source.