Running BRB-SeqTools on Mac OS

The Mac version of BRB-SeqTools has been tested on Mac OS El Capitan (10.11) and Sierra (10.12). To check your Mac OS version, go to the Apple menu and click About this Mac. This will display the Mac OS version, total memory, etc. The available storage information can also be found on the 'Storage' tab.

macos overview macos storage

Download and Launch BRB-SeqTools

download button (version 1.2, macOS only)

After downloading BRB-SeqTools, the zip file will be automatically extracted and a new folder seqtools-dl will be created. This new directory contains the following files:

  • SeqTools: GUI version of the application
  • seqtools_dge/seqtools_vc: CLI version of the application
  • samples.txt: template of samples.txt (tab-delimited)
  • samples_gatk.txt: template of samples.txt (tab-delimited) for GATK variant calling
  • examples.txt: examples of using the seqtools_dge/seqtools_vc programs

The BRB-SeqTools application (SeqTools) can be executed immediately by double clicking its icon. Users can also drag and drop the SeqTools icon to the Applications folder in order to quickly access it the next time.

Note that you may get an alert dialog that says "SeqTools can’t be opened because it is from an unidentified developer". This is a security feature called GateKeeper. To temporarily get around the alert message, you can

  1. To Right-click (or control-click) the application in question and choose “Open”
  2. Click the “Open” button at the next dialog warning to launch the app anyway

A screenshot of the program is given below: Seqtools in macOS

Software Setup

Some software requires users to accept their agreement in order to use them. We give detailed instruction below for users to follow.

1. Xcode

Xcode is an integrated development environment for macOS containing a suite of software development tools developed by Apple for developing software for macOS and other mobile operating systems. Xcode is needed in order to install other software (Tophat2, Bowtie2, etc).

Launch the Terminal (use the keyboard shortcut 'Command + Space' and enter 'terminal') and type the following 

$ xcode-select --install
A software update popup window will appear and ask you if you like to install the tools. Click the Install button to install the command line developer tools and wait it to finish. After the installation has finished, you will see a message The software was installed. You can click the 'Done' button to dismiss the message. You don’t need to click "Get Xcode"; it is used to get the full Xcode package which we don't need. Note that if the command line installation method failed for any reason, you can still install Xcode by going to the Xcode website and follow the instruction there to install Xcode.

Users can check if the development tools has been installed succesfully by using the xcode-select command with -p option. 

$ xcode-select -p
/Library/Developer/CommandLineTools

2. JDK

Java developement kit is required for running analyses like Picard. To download it, users should go to the Java Development Kit website, check Accept License Agreement and selct the file coresponding to Mac OS X. As of this writing, the download file is called jdk-8u121-macosx-x64.dmg.

After downloading the file, you can double click the file and follow the instruction to install the software. Once the installation has finished, you can verify if JDK is installed successfully by opening a terminal and type java -version. You shall see an output similar to the following: 

$ java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

3. Automatic setup script

After command line developers tools from Xcode has been installed, users can execute the following line in order to install public domain software used by BRB-SeqTools: 

$ curl -L -s https://brb.nci.nih.gov/seqtools/install_rnaseq_mac.sh | \
  sudo bash /dev/stdin | tee install_rnaseq_mac.log
After entering your password, the script will start to install software. At the end of the installation, you are asked to press the Enter key to exit the script. If you get any error message when the script exited (e.g. a network problem occurred), the installation is not complete. Please check the log file install_rnaseq_mac.log for more information.