Installation of Perl and BioPerl with modules for MySQL databases (Windows XP)

Transcription

1 Installation of Perl and BioPerl with modules for MySQL databases (Windows XP) 1. Installation of ActiveState Perl 1 2. Installation of Perl modules and BioPerl 2 3. Executing Perl scripts 5 4. Installation of the programming editor Proton 7 5. Installation of the programming editor Komodo Edit 8 1. Installation of ActiveState Perl Perl is a script programming language often used for bioinformatics solutions. There are many modules available at the Perl script archive CPAN. A special BioPerl project provides extended functions for bioinformatics. The well-established Windows version provided by ActiveState is ActivePerl The new Perl branch 5.10 was launched recently and the newest ActiveState Perl version published is now This version is one of the first of the 5.10 developmental branch, it may have some yet undiscovered problems. Some BioPerl libraries originally did not work with the 5.10 version, however, most problems are now solved and the BioPerl community has now published a new guide for the Perl 5.10 series and we suggest therefore using the newest Perl branch. Binaries for Perl 5.10 are available for installation. Download procedure: - Visit the download site: - Choose at the right panel "Language Downloads" "ActivePerl". - On the next page select at the "Choose from" tab the "Download" button for ("ActivePerl"). - If you want to receive informations from ActiveState report your details on the next page, else click on the "Continue" button. - On the next page select the required Perl package for download. For a standard Windows distribution we suggest to use the "Windows(x86)" "MSI" package of "ActivePerl " (status of December, 19 th, 2007): ActivePerl MSWin32-x msi KB "ActivePerl " (status July, 17 th, 2008): ActivePerl MSWin32-x msi (status July, 17 th, 2008). Perl Installation Jul

2 Warning: It is a good idea to remove any previous Perl installation, before installation of a new ActiveState Perl version. Delete also all previous installed packages (e.g. directory /Perl/site), since deinstallation of the main program will not touch preinstalled packages at the /site subdirectory. Be aware that packages of the 5.10 series are not binary compatible with packages of the 5.8 series and vice versa. If you update to the 5.10 series from 5.8 please update also all previous installed packages. The installation should be done using administrator rights. ActivePerl MSWin32-x msi During installation we suggest to change the preset folder from C:\Perl to C:\Program Files\Perl and to register the Perl program folder in the system path. This allows Windows to start Perl scripts ending with ".pl" by double clicking on them. Check the correct entry in the Windows PATH environment variable: Add at Control Panel System Advanced lower tab Environment variables lower window system variable Path "Edit" Add at end of line a semicolon ; and C:\Program Files\Perl\bin and additionally at end of line ; and C:\Program Files\Perl\site\bin and click OK and restart the PC. Hint: The installation program may have added these directories to the path already, but check for any double entries of older versions and remove them. The local Perl Help files are best viewed using your favourite web browser by loading the local index file: file:///c:/program Files/Perl/html/index.html 2. Installation of Perl modules and BioPerl To use MySQL and BioPerl additional modules have to be installed. These Perl modules (packages) can be downloaded from the module archive CPAN. For Windows Perl, the Active State module repository should be used. Some of the modules (like DBD-mysql or the BioPerl packages) are not provided by ActiveState and may be installed from alternative repositories: A help file for a installed specific module can be reached from the Perl Help files main window, scrolling down the left panel to the module section: (C:\Program Files\Perl\html\index.html). Some modules have a documentation called from the cmd window by entering Perl Installation Jul

3 "perldoc module" e.g. module "perldoc cwd" to read the documentation of the package "cwd" allowing to read the current directory. You can enlarge the cmd window vertically using your mouse, clicking at the upper or lower window border and pulling it up or down. The module documentation is listed page for page. Pressing "Enter" will show the next line, pressing the "space" tab the next page. For communication wit a MySQL database four additional modules are needed: DB_File DBI Data-Table DBD-mysql the Berkeley database management module (DBD) the common database interface the database table handling routines the MySQL-driver for trhe DBD database system The ActiveState Repository does not hold the newest version of BioPerl. We suggest to use the new distribution provided by the BioPerl community. Some BioPerl programs may not work with the 5.10 Perl branch (e.g. Bio::SeqIO::entrezgene). This may be updated soon and we suggest to use already the 5.10 branch. Prerequisite: for ActiveState at least Perl version >= A new BioPerl Wiki for installation on Windows guides through the installation process: Module installation procedure using ppm: Run the module installation tool Perl package manager ppm: "Start" "Run" "cmd" "ppm" # Starts the Perl package manager ppm uses a convenient graphical interface in the newest Perl versions. Configuration of additional repositories: Select at the main menu item "Edit" "Preferences" tab "Repositories" Copy "Name:" and "Location:" (internet link) into the respective entry fields. Do not change "Suggested:" "Install PPM-Repositories". Click on "Add" button to activate them. For the Perl 5.8 branch: Name BioPerl-Regular Releases Kobes Location Perl Installation Jul

4 Bribes For the Perl 5.10 branch: Name BioPerl-Regular Releases Kobes Bribes Trouchelle Location Select at the menu item View All Packages. Enter at the "magnifying glass symbol" entry field the module names, select them, and start the installation by selecting menu item Action Install. Current suggested modules are: MySQL database support: DB_File v DBI v (preinstalled at Perl 5.10) DBD-mysql v (for 5.10 Kobes repository) Data-Table v 1.54 BioPerl (BioPerl, Kobes and Bribes repositories) bioperl bioperl-db bioperl-network bioperl-run v 1.5.2_100 BioPerl package v 1.5.2_100 BioPerl database packages v 1.5.2_100 BioPerl pathway packages v 1.5.2_100 BioPerl application packages Only for Perl 5.8 series (not recommended): bioperl v BioPerl bioperl-gui v 0.7 BioPerl graphical user interface Graphics support GD v 2.39 (preinstalled in Perl ) Support for graphical user interfaces (GUI) and Windows system calls Win32-API v 0.55 (not preinstalled in Perl 5.8) Win32-GUI v 1.06 Tk v (not preinstalled in Perl 5.10) Excel Spreadsheet support Spreadsheet-ParseExcel v0.32 Perl Excel file reader Perl Installation Jul

5 Spreadsheet-ParseExcel-Simple v1.04 Perl Excel file reader Spreadsheet-ParseExcel_XHTML v1.04 Perl Excel XHTML file reader Spreadsheet-WriteExcel v2.21 Perl Excel file writer (for 5.10 Trouchelle) SOAP protocol support for internet connection to SOAP services SOAP-Lite v 0.69 Web service package You can always visit, verify and update module installations using ppm. Checking the installed version of BioPerl A version number can be called by a "one-liner", a Perl command which is typed or copied into one line of the Windows cmd terminal: The Linux version is found at the BioPerl FAQ internet page: perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' For the Windows cmd terminal the single quotes enclosing the red labelled executable command must be changed to double quotes ' ", and the double quotes around the line break symbol "\n" must be escaped by back slashes: \"\n\". The modified one-liner for Windows reads: perl -MBio::Root::Version -e "print $Bio::Root::Version::VERSION,\"\n\"" Click on the "Start" tab of the Windows main window, select the "Run" option and type "cmd" in the prompted entry field. In the cmd window right-click onto the "C:\"- symbol in the left upper corner of the window and select the menu item "Edit" "Paste" and insert the one-liner modified for Windows and press "Enter". The Perl interpreter should return the installed BioPerl version: " " (= version ). The subversions are separated by several zeros (00). 3. Executing Perl scripts Run a script by double clicking on it: A convenient way is to start a Perl script by double clicking on its file using Windows Explorer. It should be shown with a gecko symbol and has always the ending ".pl". You can also make a desktop link to a script, you may use often. This will allow the script to ask for programmed parameters, run the script job and close again the script window. If you do not want to evaluate script changes, this is best. However, you will not be prompted with error messages. Perl Installation Jul

6 The provided script version2.pl will popup the versions of installed Perl and BioPerl programs. Press "Enter" to close the program. Copy it e.g. in a directory "D:\perl_scripts" and execute it. The result should read: This is Perl v This is BioPerl v Run a script by calling it at the command line of cmd.exe: To start a Perl script with a command line window, select at Windows Start button "Start" "Run" "cmd". Move to the directory of the Perl script, by changing drive and path: Directories with spaces should be stated in quotes like "Program Files". You can use following commands to navigate in your directory tree: D: this will select drive D cd \perl_scripts this will move to the directory cd.. will go back one directory level dir will list files in a directory Start the script by calling it from \perl_scripts: perl script.pl e.g. perl version2.pl Using the history function (cursor up or down keys) you can recall earlier typed commands. Now you can follow script comments and error messages, while running the script. The error message will show the script line most likely containing the error. You can always stop a script by typing "Ctrl + C". Using a c.bat batch file to start a command window Make a small batch file called e.g. "c.bat" in the current directory to start a command window in the current directory holding following text: cmd By double-clicking on c.bat a command window will open in the current directory. Now you can execute the script by typing its name: "version2.pl". If your Perl interpreter is not registered correctly in the Windows path variable, you may start the script typing "perl version2.pl". Perl Installation Jul

7 4. Installation of the programming editor Proton (German) Special editor programs may be helpful for writing Perl code by formatting code elements in different colours. A small and convenient freeware editor, which can be used to manage huge files or edit scripts is Proton Version 3.2 from U. Meybohm: Just unzip the downloaded installation file and copy it in a directory like "C:\Program Files\Proton". You can make a desktop link to the file "proton.exe" in the installation directory. (Right click on the file using Windows Explorer and select "Send to" "Desktop". Start Proton by clicking on the symbol. In the menu item "syntax scheme" a scheme can be activated, if not already detected automatically, to show Perl scripts, SQL queries or many other programming languages with very useful different colouring of text, parameters, functions and comments. Also line numbers are indicated for easy tracking of programming errors. Select "Perl" for Perl scripts. For MySQL scripts best "SQL(Oracle)" is used as a scheme. Shortcut from Proton to start a Perl script just edited: A Perl script can be started from Proton by defining a shortcut like "Ctrl + F5". Select menu "Shortcut" and "Define shortcut" and assign a free shortcut (Ctrl + F5). Name the shortcut like "Execute Perl script". At the command field enter: command.com /k perl "%A%" This will start a command window with the current script and within the current path. During writing a script, it can be tested by using this shortcut. For closing the command window type "exit" into it. Hint: Do not fotget to save your changes before executing the script. A more convenient method is to open in parallel an independent command window of cmd.exe and use it to run the script. You can always restart the script using the history function of the command line (The "Cursor Up" or "Cursor Down" keys will recall previously typed commands). Best use the c.bat script batch file as Perl Installation Jul

8 described above to restart the command window. ou can easily jump between the command window and Proton using "Alt+Tab". Opening big FASTA files Very big files (above 10 MB) will crash the Windows editor notepad.exe regularely. However, Proton will manage them (dependent on RAM size) quite good. Using a "Send to" Link for Proton It is a good idea to copy a link for Proton in your personal "Send to" folder. Eventually you have to activate the view of hidden directories using the Windows Explorer to find this folder (Explorer menu item "Options" "Folder settings" "View" "Hidden files and folders / Show all files and folders" and "Show content of system folders". The folder should be found at: "C:\Documents and Settings\your_login_name\Send to" Now you can send a file to Proton by using the right mouse button on a selected file and choosing "Send to" "Proton". 5. Installation of the programming editor Komodo Edit ActiveState provides a free version of the editor of their development environment Komodo, the "Komodo Editor v 4.4.1", which can be used for editing Perl scripts. It has many additional functions not present in Proton useful for Perl programming, like matching of leading and lagging parentheses and spell checking. Download address: Click on the blue "Get Komodo Edit" button and on the next page on the "Free" Download button. You are prompted for optional personal details. Click on "Continue" button and select the Windows "MSI" package (27.8 MB). Komodo-Edit msi KB Log in as an administrator and install the program using the standard settings suggested. You can start the editor by clicking on the "Komodo Edit 4" symbol generated on the desktop. You can also add a shortcut to your "Send To"-Folder as described above for Proton. Loading and starting a script from Komodo editor: You can use the menu item "File" "Open" to load a script or you point at a file rightclicking your mouse and sending it to Komodo, in case you have added a link to Perl Installation Jul

9 your "Send To" folder. Best Select at main menu item "View" "View Line numbers" (Hit the key combination "Ctrl+Shidt+4" for toggling). For executing a script in a new command line window for testing it during programming a shortcut can be generated and combined with the command window: - Select main menu item "Tools" "Run Command" ("Ctrl+R") to open the "Run Command" window. - At the left-pointing arrow-button left of the "Run" entry filed select "%(perl) : Configured Perl interpreter" - Click into the entry field and add a "space" behind "%(perl)" - Now select as before "%F : File path" - The entry filed should now read: "%(perl) %F". - Click on the "More" button to view advanced options - At "Advanced Options" "Run In:" select "New console". - Click on the "Run" button. - For closing the command window hit any key. Version Last edited Jul Perl Installation Jul