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| ## Table of Contents | ||
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| * [2022 update](https://github.com/rrwick/Bandage#2022-update) | ||
| * [Intro](https://github.com/rrwick/Bandage#intro) | ||
| * [Help](https://github.com/rrwick/Bandage#help) | ||
| * [Pre-built binaries](https://github.com/rrwick/Bandage#pre-built-binaries) | ||
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| * [Credits](https://github.com/rrwick/Bandage#credits) | ||
| * [License](https://github.com/rrwick/Bandage#license) | ||
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| ## 2022 update | ||
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| Bandage is now about seven years old! Despite its popularity, I sadly don't have the time to give it the attention it deserves. Also, its codebase is too large and my C++/Qt skills are too rusty for me to make anything more than trivial changes. | ||
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| I'm not declaring Bandage completely abandoned, because I still think it's a useful tool, but don't expect a lot development or support on this repo. I will, however, strive to ensure that Bandage continues to run well on modern systems. E.g. I released [v0.9.0](https://github.com/rrwick/Bandage/releases/tag/v0.9.0) in January 2022, which compiles using modern versions of [Qt](https://www.qt.io/) and runs natively on Apple Silicon Macs. | ||
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| ## Intro | ||
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| Bandage is a GUI program that allows users to interact with the assembly graphs made by *de novo* assemblers such as <a href="https://www.ebi.ac.uk/~zerbino/velvet/" target="_blank">Velvet</a>, <a href="http://bioinf.spbau.ru/spades" target="_blank">SPAdes</a>, <a href="https://github.com/voutcn/megahit" target="_blank">MEGAHIT</a> and others. | ||
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| More information and download links are on the Bandage website: <a href="http://rrwick.github.io/Bandage/" target="_blank">rrwick.github.io/Bandage</a> | ||
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| ## Help | ||
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| Bandage documentation is available on the <a href="https://github.com/rrwick/Bandage/wiki" target="_blank">Bandage GitHub wiki</a>. | ||
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| Bandage help tips are also built into the program. Throughout the UI, you will find these icons next to controls and settings: <img src="http://rrwick.github.io/Bandage/images/helptext.png" alt="help text icon" width="16" height="16">. Click them to see a description of that element of Bandage. | ||
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| ## Pre-built binaries | ||
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| Compiled 64-bit binaries for Ubuntu Linux, CentOS, OS X and Windows are available in the GitHub <a href="https://github.com/rrwick/Bandage/releases/" target="_blank">'Releases' section</a> and from the <a href="http://rrwick.github.io/Bandage/" target="_blank">Bandage website</a>. | ||
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| If you download and run the Mac binary, you may receive a warning stating that Bandage 'can't be opened because it is from an unidentified developer.' Right click on the file and select 'Open' to override this warning. | ||
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| The Linux binaries comes in two varieties: dynamically-linked and statically-linked. The dynamically-linked binary is preferable, but it has more dependencies (like Qt 5). If you experience problems with the dynamically-linked binary, please try the statically-linked version instead. | ||
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| ## Building from source | ||
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| If the compiled binaries do not work for you, the instructions below should help you build Bandage on most common OSs. If you are having difficulties building Bandage for your OS, feel free to contact me (Ryan) at [email protected] and I'll do my best to help you out! | ||
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| ### <img src="http://rrwick.github.io/Bandage/images/OS/ubuntu.png" alt="" width="34" height="40" align="middle"> Ubuntu | ||
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| The following instructions successfully build Bandage on a fresh installation of Ubuntu 14.04: | ||
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| 1. Ensure the package lists are up-to-date: `sudo apt-get update` | ||
| 2. Install prerequisite packages: `sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev libgl1-mesa-dev` | ||
| 3. Download the Bandage code from GitHub: `git clone https://github.com/rrwick/Bandage.git` | ||
| 4. Open a terminal in the Bandage directory. | ||
| 5. Set the environment variable to specify that you will be using Qt 5, not Qt 4: `export QT_SELECT=5` | ||
| 6. Run qmake to generate a Makefile: `qmake` | ||
| 7. Build the program: `make` | ||
| 8. `Bandage` should now be an executable file. | ||
| 9. Optionally, copy the program into /usr/local/bin: `sudo make install`. The Bandage build directory can then be deleted. | ||
| ## Pre-built binaries | ||
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| ### <img src="http://rrwick.github.io/Bandage/images/OS/linux.png" alt="" width="34" height="40" align="middle"> Other Linux distributions | ||
| Compiled 64-bit binaries for Ubuntu Linux, CentOS, macOS and Windows are available in the GitHub <a href="https://github.com/rrwick/Bandage/releases/" target="_blank">'Releases' section</a> and from the <a href="http://rrwick.github.io/Bandage/" target="_blank">Bandage website</a>. | ||
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| If your Linux distribution is sufficiently similar to Ubuntu (e.g. Linux Mint), I recommend trying the Ubuntu build instructions above. Otherwise, try the 'Using Qt Creator' instructions below. | ||
| If you download and run the Mac binary, you may receive a warning stating that Bandage 'can't be opened because it is from an unidentified developer' or 'is damaged and can't be opened'. Right click on the file and select 'Open' to override this warning. If that doesn't work, clear the quarantine extended attribute via the command line with `xattr -cr Bandage.app`. | ||
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| ### <img src="http://rrwick.github.io/Bandage/images/OS/apple.png" alt="" width="34" height="40" align="middle"> Mac | ||
| The Linux binaries come in two varieties: dynamically-linked and statically-linked. The dynamically-linked binary is preferable, but it has more dependencies (like Qt 5). If you experience problems with the dynamically-linked binary, please try the statically-linked version instead. | ||
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| The following instructions successfully build Bandage on OS X 10.8 and later: | ||
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| 1. Install Xcode, along with the Xcode Command Line Tools. If you can run the `clang` command from the terminal, you should be good to continue. | ||
| 2. Install Qt 5. This is most easily done using Homebrew: <a href="http://brew.sh/" target="_blank">brew.sh</a>. Install the Qt 5 package with this command: `brew install qt5`. | ||
| 3. Download the Bandage code from GitHub: `git clone https://github.com/rrwick/Bandage.git` | ||
| 4. Open a terminal in the Bandage directory. | ||
| 5. Run qmake to generate a Makefile. The location of the `qmake` command may vary, depending on how Qt was installed. If you used Homebrew, it should be here: `/usr/local/opt/qt5/bin/qmake`. | ||
| 6. Build the program: `make` | ||
| 7. `Bandage` should now be an application bundle. | ||
| 8. Optionally, copy the Bandage application bundle into the 'Applications' folder and delete the Bandage build directory. | ||
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| ### <img src="http://rrwick.github.io/Bandage/images/OS/qt.png" alt="" width="34" height="40" align="middle"> Using Qt Creator | ||
| ## Building from source | ||
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| For Windows and some Linux distributions, the easiest way to build Bandage from source is by using Qt Creator, the Qt IDE. I successfully used this procedure has been used on Windows and on CentOS 6.7. It should also work for Ubuntu Linux and OS X. | ||
| If the compiled binaries do not work for you, you can build Bandage on most common OSs using [Qt](https://www.qt.io/): | ||
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| 1. Set up a compiler. | ||
| * For Windows, you can use the Microsoft Visual C++ compiler by installing <a href=" https://www.visualstudio.com/" target="_blank">Visual Studio</a>. Alternatively, you can skip this step and the Qt installation will provide the MinGW compiler. | ||
| * For CentOS, this can be done quickly using the yum package manager: `yum install gcc-c++` | ||
| * <a href="http://doc.qt.io/qt-5/supported-platforms.html" target="_blank">Look here</a> for more information on Qt supported compilers. | ||
| 2. Install the Qt SDK: <a href="http://www.qt.io/download-open-source/" target="_blank">www.qt.io/download-open-source</a>. The disk space required can be reduced by unticking the iOS and Android options in the Qt installer. | ||
| 3. Download the Bandage code from GitHub: | ||
| * Either clone using: `git clone https://github.com/rrwick/Bandage.git` | ||
| * or download from here: <a href="https://github.com/rrwick/Bandage/archive/master.zip" target="_blank">https://github.com/rrwick/Bandage/archive/master.zip</a> | ||
| 1. Make sure you have a compiler and other common developer tools set up. | ||
| * For macOS, this means Xcode and its command line tools. | ||
| * For Ubuntu: `sudo apt install build-essential git libgl1-mesa-dev libxcb-xinerama0` | ||
| 2. Install the [Qt SDK](https://www.qt.io/download-open-source) with version 5.15 or later. Double check that you install a version compatible with your OS ([Qt 5 supported platforms](https://doc.qt.io/qt-5/supported-platforms.html) and [Qt 6 supported platforms](https://doc.qt.io/qt-6/supported-platforms.html)). | ||
| 3. Clone the Bandage code from GitHub: `git clone https://github.com/rrwick/Bandage.git` | ||
| 4. Open the Qt Creator program and load the `Bandage.pro` file which is in the Bandage directory. Since this is the first time the project has been loaded, it will ask you to configure the project. The defaults should be okay, so click 'Configure Project'. | ||
| 5. Change to the release build configuration by clicking where it says 'Debug' in the bottom left area of Qt Creator and select 'Release'. | ||
| 6. Build and run Bandage by clicking the green arrow in the bottom left area of Qt Creator. Bandage should open when the build has finished. | ||
| 7. You will find the executable file in a new folder that begins with 'build-Bandage-Desktop'. | ||
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| ## Contributing | ||
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| New contributors are welcome! If you're interested or have ideas, please contact me (Ryan) at [email protected]. | ||
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| ## Citation | ||
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| If you use Bandage in your research, please cite the following publication: | ||
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| [Wick R.R., Schultz M.B., Zobel J. & Holt K.E. (2015). Bandage: interactive visualisation of de novo genome assemblies. Bioinformatics, 31(20), 3350-3352.](http://bioinformatics.oxfordjournals.org/content/31/20/3350) | ||
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| ## Credits | ||
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| Bandage makes use of the <a href="http://www.ogdf.net/" target="_blank">OGDF</a> library for performing graph layout algorithms. My thanks goes out to the OGDF developers for their excellent work! | ||
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| I also thank <a href="https://github.com/rchikhi" target="_blank">Rayan Chikhi</a> and <a href="https://github.com/epruesse" target="_blank">Elmar Pruesse</a> for their contributions to the code. | ||
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| ## License | ||
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| GNU General Public License, version 3 | ||