C-mii Installation Guide Copyright ISL, BIOTEC

Transcription

1 1 C-mii Installation Guide Copyright ISL, BIOTEC

2 2 Table of Contents Page 1. System Requirements 3 2. How to download C-mii installer 3 3. How to Install C-mii on Windows Platform 4 4. How to Install C-mii on Ubuntu Linux Platform How to Uninstall C-mii 16

3 3 1. System Requirements Minimum System Requirements Processor: 1.8 GHz of dual core processors OS: Windows XP/ Windows Vista/ Windows 7 /Ubuntu Linux Memory: 2 GB Hard Disk: 4 GB free space Recommended System Requirements Processor: 2.66 GHz of quad core processors OS: Windows XP/Ubuntu Linux Memory: 4 GB Hard Disk: 8 GB free space 2. How to Download C-mii Installer To download C-mii, please go to The download page will redirect to the page showing a list of installers (Figure 2.1). Figure 2.1 C-mii download page

4 4 3. How to Install C-mii on Windows Platform 3.1 C-mii setup wizard First, extract the c-mii_setup.zip to get the C-mii setup folder. Next, go into Cmii_setup folder and double click on the Wizard (Figure 3.1) and then click on the License Agreement page. (setup.exe) to open the C-mii Setup to read the terms of license agreement Figure 3.1 C-mii setup wizard screen

5 5 3.2 Terms of License Agreement C-mii software is distributed under the GNU General Public License. Please carefully read the terms of license agreement before starting the installation. If you accept terms of the license agreement, click to continue the installation or click to cancel the installation (Figure 3.2). Figure 3.2 License agreement screen 3.3 Location for C-mii installation Next step, you need to specify the home directory in your machine for C-mii installation. C-mii requires about 2.0 Gigabytes free space. The default directory for software installation is located in C:\C-mii directory. You could install in a different directory by clicking to select another directory (Figure 3.3). After specifying the location to install, click to continue.

6 6 Figure 3.3 Browse for installation location screen

7 7 3.4 Start Menu Folder Selection In this step, you need to select the start menu folder for the C-mii shortcut (Figure 3.4) or use the default folder (c-mii folder). After folder is selected, click to continue to the next step. Figure 3.4 Start menu folder selection screen 3.5 Required Components Installation In order to successfully start and run C-mii, you need to install all required external software and database components. The easiest way to install is via the typical installation, where all components are checked for installing by default. (Figure 3.5). The installer will install only missing components and components with newer version. C-mii requires six software components including BLAST, Ghostscript, JDK, Perl, Python, and UNAFold.

8 8 Figure 3.5 Software component installation screen BLAST Installation If BLAST does not exist, the installer will install the standalone BLAST (version ) on your machine.

9 JDK (Java SE Development Kit) Installation After installing BLAST, the installer will continue the installation by extracting JDK installer. You need to perform the following steps to complete JDK installation: - Accept the JDK license agreement by clicking on button - Select the program feature as development tools, and then click to continue the installation - Choose the destination folder or use the default directory for java installation The screen of complete installation is shown in Figure 3.6. Figure 3.6 The complete JDK installation screen

10 Perl Installation You could perform the following steps to complete ActivePerl installation: - Accept the ActivePerl license agreement by clicking on button - Select setup feature and specify the directory for installing ActivePerl - Choose optional setup actions and click on button to start the installation The screen of complete installation is shown in Figure 3.7 Figure 3.7 The complete ActivePerl installation screen

11 Python Installation The Python installation is simple by selecting a directory and choosing installation features (Figure 3.8). Figure 3.8 The Python feature selection screen

12 UNAFold Installation UNAFold [ is a software for predicting the RNA secondary structure developed in Perl programming language. To install UNAFold, specify a destination directory and click (Figure 3.9). Figure 3.9 The UNAFold installation screen

13 Ghostscript Installation Ghostscript is an interpreter for the PostScript language and PDF. To install Ghostscript, click to select the directory or use the default directory, and then click to start the installation (Figure 3.10). Figure 3.10 The Ghostscript installation screen

14 Database Installation To use standalone BLAST, the installer will automatically create BLAST databases in your machine. All sequence files would be copied and the databases will be built through formatdb command. Three types of databases are required by C-mii: mirna database contains plant mature mirna sequences obtained from mirbase release 16 [ Non-coding RNA database contains non-coding RNA sequences obtained from Rfam release 10 [ with the exclusion of mirnas. Protein databases contain protein sequences obtained from UniProt [ including - UniProtKB/Swiss-Prot (plants only) (release 2010_12) - UniProtKB/TrEMBL (plants only) (release 2011_01)

15 15 4. How to Install C-mii on Ubuntu Linux Platform Please make sure that your machine is connected to the Internet. Then, follow below steps to install C-mii. 4.1 Copy c-mii.tar.gz into a directory which will be the parent directory of C-mii and then extract the file using the following command. tar zxvf C-mii.tar.gz 4.2 Change directory to the c-mii directory and install all C-mii required components using the following commands. cd c-mii sh install.sh Notes: (1) The installation may take a long time during the building of BLAST databases via formatdb. (2) For java installation, please use tab key to enable the accept button for the license agreement. 4.3 To start C-mii, please go to c-mii directory, then double click on c-mii.sh and run it from the terminal.

16 16 5. How to Uninstall C-mii 5.1 Windows Platform To uninstall C-mii from Windows machine, click start >> All Programs >> c-mii >> Uninstall c-mii (Figure 5.1). All installed C-mii s files will be removed. Figure 5.1 C-mii uninstallation on Windows Platform

17 Linux Platform To uninstall C-mii from Ubuntu Linux, please remove folder C-mii from your machine.