Windows Installation Guide
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1. Introduction Systems-Level Interactive Data Exploration (SLIDE) is a user-driven interactive visualization tool for largescale –omics data. SLIDE can organize and visualize quantitative –omics data in expression based heatmaps on a standard web browser. It allows users to interactively navigate through the heatmaps and create sub-analyses of selected feature sets. It can be used to visualize the data at different levels of granularity through multiple simultaneous views. This manual is a step-by-step installation and configuration guide for running SLIDE on Microsoft Windows. 2. Installation 2.1 System requirements SLIDE has been tested on various systems. The table below shows a typical system configuration that would work well with SLIDE: Operating System Windows 10 or Windows 7 CPU Intel Xeon CPU E5-1620 v4 @ 3.50 GHz Intel Core i7-6700HQ CPU @2.60 GHz Intel Core i7-4600U CPU @2.10 GHz 16 GB RAM Microsoft Internet Explorer (recommended) Memory Web browser 2.2 Prerequisites SLIDE requires the following software to be available on the system before you can configure it to run. To install the prerequisites you must have administrative permissions. For detailed instructions with screen captures on installing the prerequisites, see section 2.5. The process is also briefly described below. Java Development Kit (JDK) http://www.oracle.com/technetwork/java/javase/downloads/jdk8downloads-2133151.html For 32-bit systems, jdk-8uxxx-windows-i586.exe is the JDK installer For 64-bit systems, jdk-8uxxx-windows-x64.exe is the JDK installer Detailed instructions for JDK installation for Microsoft Windows are available here. GlassFish Server http://download.oracle.com/glassfish/4.1.1/release/index.html 1. Download glassfish-4.1.1.zip 2. Unzip the folder 3. Place it in your preferred installation directory A detailed GlassFish server installation guide can be found in Page 12 of this document. MongoDB https://www.mongodb.com/download-center#community MongoDB requires creating a specific directory that it uses as its repository. Create data\db directories in the same drive where MongoDB was installed to set up the MongoDB environment as shown in Figure 8. Detailed instructions for Windows MongoDB installation can be found here. Python https://www.anaconda.com/download/#windows Download Python 3.6, 64-bit or 32-bit depending on system architecture. Detailed installation instructions for Anaconda’s implementation of Python are available here. Note: Select the option ‘Add Anaconda to my PATH environment variable’ during installation as shown in Figure 10. Numpy (Python Package) Anaconda’s implementation of Python has Numpy pre-installed, so no additional configuration steps are required here. For other implementations of Python Numpy may have to be installed separately. Scipy (Python Package) https://anaconda.org/anaconda/scipy To install Scipy: 1. Start ‘Command Prompt’ with administrator privileges as shown in Figure 1. 2. Issue the following command: conda install –c anaconda scipy fastcluster (Python Package) https://anaconda.org/conda-forge/fastcluster To install fastcluster 1.1.23 use the following command in ‘Command Prompt’: conda install –c conda-forge fastcluster After the dependencies are installed, go to Section 2.3 for instruction on how to download and configure SLIDE. 2.3 SLIDE Download and Configuration SLIDE can be downloaded from https://github.com/soumitag/SLIDE/raw/master/application/slide.zip. To install SLIDE unzip slide.zip into your preferred installation directory. To setup SLIDE: Open a Command Prompt (as administrator) Figure 1. Start Command Prompt as administrator Figure 2. Configuring SLIDE 1. Run the configure_slide.bat file located inside the slide folder. To run the .bat file use the following command (as marked in 1 and 2 of Figure 2): configure_slide.bat 2. On running the .bat file you will be prompted to enter the following information: a. Path to Java Installation Directory Provide the path to the folder containing the target java.exe on your system as shown in 3 of Figure 2. b. Path to GlassFish Server Installation Directory Provide the path to the “bin” folder inside the GlassFish Server Installation Directory as shown in 4 of Figure 2. c. Path to MongoDB Installation Directory Provide the path to the “bin” folder inside the target MongoDB installation directory as shown in 5 of Figure 2. d. Path to Python Installation Directory Provide the path to the directory containing the target python.exe file as shown in 6 of Fig. XX. Figure 3. Updating asenv.bat to set the Java used by GlassFish 3. Set JDK path used by GlassFish Server Append the following line to the asenv.bat file as shown in Fig. XX: SET AS_JAVA=C:\Program Files\Java\jdk1.8.0_144 (where C:\Program Files\Java\jdk1.8.0_144 is the path to your JDK installation. Note that this path does not include the “bin” folder) The asenv.bat file can be found in the glassfish\config folder inside GlassFish installation directory. For instance, if GlassFish is installed on your PC at: C:\Program Files\glassfish-4.1.1 the asenv.bat file can be found at C:\Program Files\glassfish-4.1.1\glassfish\config\asenv.bat. 2.4 Start and Stop SLIDE To start SLIDE run slide\bin\start-slide.bat. To start using SLIDE open Microsoft Internet Explorer and go to http://localhost:8080/VTBox/. To stop SLIDE run slide\bin\stop-slide.bat. 2.5 Installing Dependencies 2.5.1 JDK Installation Download the appropriate JDK 1.8 from http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html For 32-bit systems, download jdk-8uxxx-windows-i586.exe For 64-bit systems, download jdk-8uxxx-windows-x64.exe In the following figure, jdk-8u144-windows-x64.exe is for the 64-bit systems. Figure 4. JDK1.8 download 2.4.2 GlassFish Server Installation To download GlassFish Server go to http://download.oracle.com/glassfish/4.1.1/release/index.html and follow the steps shown in Figures 5 and 6. Figure 5. GlassFish Server download step 1 Figure 6. GlassFish Server download step 2 2.4.3 MongoDB Installation Download the Windows MongoDB installation from https://www.mongodb.com/downloadcenter#community as shown in Figure 7. Figure 7. MongoDB download MongoDB requires creating a specific directory that it uses as its repository. Create the data\db directories in the same drive where MongoDB was installed to set up the MongoDB environment, as shown in Figure 8. Figure 8. Creating data\db folder structure in same drive where MongoDB is installed 2.4.4 Anaconda Python Installation Download Python 3.6, 64-bit or 32-bit depending on your system architecture from https://www.anaconda.com/download/#windows. During installation, select the option to add Anaconda to the system PATH variable as shown in Figure 10. Figure 9. Anaconda download Figure 10. Select the option to add Anaconda to the system PATH variable 2.4.5 Scipy Installation For the installation of Python package Scipy, open a Command Prompt as administrator as shown in Figure 1. Issue the command as highlighted in red in Figure 11. Figure 11. Conda install Anaconda Scipy 2.4.6 fastcluster Installation For the installation of Python package fastcluster, open a Command Prompt as administrator as shown in Figure 1. Issue the command as highlighted in red in Figure 12. Figure 12. Conda install fastcluster package
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