'phred dist acd.tar.z'

Transcription

1 Phred is free for academic use but does require registration and for you to obtain a licence. Please visit and follow the instructions. A copy of the Phred source code will be sent to you by . (Please note, processing Phred licences at the University of Washington can take up to two weeks) You will be sent two files by , and the one you need is called 'phred dist acd.tar.z' To use Phred on Windows please follow the instructions below instead of those included in the . The installation process for Phineus is as follows Phred PostgreSQL JAVA Phineus Phred Compiling the code 1 Once you receive the Phred source code, you should extract (typically using WinZip) the files into a folder where you would like to keep the software. We recommend creating a folder on your C drive called Phred. Into that directory you also need to replace a file with a Windows specific file that will allow Phred to be built successfully. Please visit to download the file. Please unzip this file into the directory where you have just extracted Phred Should Windows prompt "would you like to replace the existing file" Click yes.' If you do not have Winzip installed you can download from the following site 2 To install Phred you will need to download and install Microsoft's free Visual C++ Express Edition. Instructions for installation of which can be found at the following address 3 Once installed, run the "Visual Studio 2005 Command Prompt", by selecting the relevant icon from your windows Taskbar start menu.

2 4 Once opened you need to navigate to the directory where you have extracted the Phred source code (e.g C:\Phred) For example, if you have extracted the Phred source code into the directory 'phred' located on your C Drive, then the command would be: cd C:\phred (press return) Now type nmake (press return). Phred is now being compiled and you will see the progress on screen once complete (you will see the command prompt) a file called phred.exe has been produced in the Phred directory.

3 Phred Setting the Environment Variable 1 Using windows, go to the control panel 2 If using Windows XP click 'Start' 'Control Panel' and change the view to 'classic view' If using Windows 2000 click 'Start' 'Settings' 'Control Panel'

4 3 Double click 'System', which will show up a window containing many TABS. Select the tab marked 'Advanced' and then click on 'Environment Variables' towards the bottom 4 Click 'New' located below the System variables box (not user variables)

5 5 Enter the following in the 'New System Variable' popup box, replacing "C:\phred" with the location you have saved phred if different. Variable name : PHRED_PARAMETER_FILE Variable Value : C:\phred\phredpar.dat 6 Click 'OK' to continue Click 'OK' in the Environment Variables dialog Click 'Apply' followed by 'OK' in the System Properties dialog.

6 PostgreSQL Phineus makes use of the free third party Database PostgreSQL to store data and settings. This allows data to be backed easily, and enables the rapid installation of new schemas and settings. PostgreSQL can be downloaded at the following site After downloading, unzip the files into a directory of your choice. Then, run the file named postgresql 8.2.msi. 1 Choose your language, Click next twice and proceed to the installation notes. As with any software you should read these notes for any issues that you may disagree with. Should you accept, Click next. 2 The installer options screen displays the default options for PostgreSQL. The standard options are sufficient for Phineus and we recommend you accept the defaults by clicking 'Next' 3 Service Configuration Postgres requires the creation of a local user account in order to run. This requires that you, or the person installing PostgreSQL has administrator access to the PC on which the install is being performed. If you do not have administrator access, or are not sure if you do, check with your local Systems Administrator, as they should be able to help. The default values selected by PostgreSQL for Service Name, Account domain (which will be your computer's name) and Account name are perfect for Phineus, however, you should provide a password for the account.

7 This password should be something that you remember and should conform to the requirements of passwords on your local area network (so if your network requires a minimum password length of 8 characters, then the postgres account will also require this). Should you enter a password that does not meet your network requirements the install will rollback and you will need to start again. Once you have provided a memorable password, press next to continue. NOTE: If the installer prompts you to create the user please click 'Yes'

8 4 Initialise database Cluster All standard settings are appropriate, other than for the Superuser name, which is the login name you will use to access the data stored by Phineus. This should be changed from its default value to root as shown in the screenshot. You can then supply a password (of any length) and finally select Next to continue with the installation. 5 Initialise procedural languages Click next 6 Enable contrib modules Click next 7 Ready to Install Click next 8 Installation complete Congratulations, PostgreSQL is now installed on your computer Click Finish

9 JAVA Phineus requires JAVA version 1.5 or above to be installed on your computer to run. To check whether you have JAVA installed, or if you do, which version, please visit the following website If you need to install JAVA or have a version less than 1.5 please follow the instructions on the website. If your version of JAVA is 1.5 or above, you can now proceed to the Phineus install.

10 Phineus 1 Double click the Phineus installer to begin 2 Welcome to the Phineus Setup Wizard Click Next 3 Licence Agreement You should read carefully the licence agreement and choose whether to accept or decline. To continue after agreement, click Next

11 4 Select Destination Location By default Phineus will be installed in your program files directory, we suggest keeping this location, however you may change the install location at this step. Once complete click Next 5 Select Start Menu Folder Click Next this will create a shortcut for you in your 'Start' menu

12 6 Select Additional Tasks At this point you can choose to create a desktop shortcut Icon for launching Phineus Click Next 7 Ready to Install Click Next

13 8 Completing the Phineus Setup Wizard Phineus is now Installed Click Finish

14 Configuring Phineus 1 Click 'Start' and navigate to the Phineus folder located in 'All Programs'. In the Phineus folder there is a shortcut named 'Configure Phineus' 2 Launch the shortcut and you will be asked to locate the Phineus Install location 3 Click OK and then navigate to the location Phineus is installed (for example C:\Program Files\Phineus') Highlight the folder named Phineus and then select 'Open' 4 Login Here you should enter the superuser details for PostgreSQL which you created when you completed that install (user root) Once you have entered your details, press Login! and the initial Phineus user databases will be created, and the system will complete the Phineus install and configuration. Please note, this can take time and when complete a pop up will be launched to let you know all has been successful. Phineus is now installed and ready for use.