If a Perl module is not available for the ActiveState version of Perl (ActivePerl), you might be able to download it from the Comprehensive Perl Archive Network (CPAN. DUCAT offers exclusive JAVA Training & Certification program with live project by industry expert In Noida,Ghaziabad,Gurgaon,Faridabad,Greater Noida,Jaipur. Webmin Updates. Listed below are updates to Webmin for problems that have been discovered since the each release. Most are in the form of modules, which can be. Biopython Tutorial and Cookbook Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy&#. ![]() This document covers compilation and installation of the Apache HTTP Server on Unix and Unix-like systems only. For compiling and installation on Windows, see Using. Downloading And Installing Perl Modules On LinuxQuick Install Guide. Installing Bio. Mart. The Bio. Mart components are. Perl API and all the Bio. Mart applications that depend on it, such as. Mart. View, Mart. Service, Mart. URLAccess and DAS Annotation Server (if. Java. API and all the Bio. Mart applications that are written in Java, such. Mart. Editor, Mart. Shell, Mart. Explorer and Mart. Builder. 1. 1 Downloading martj. Binary distribution. The best way to obtain martj. The martj- bin. zip. Windows users, and contains the Java API and all. Java- based Bio. Mart applications. The bin folder contains a. You can. unpack it using Win. Zip or a similar application. The martj- bin. tgzdistribution is identical to the martj- bin. Unix and Linux users. Instead of. . bat scripts, it contains a number of . You can unpack it using: tar - zxvf. The martj- bin. dmg. Mac. OSX users, and contains bundles in the bin. Java- based Bio. Mart applications. The. bin folder also contains the Mart. Shell application . Mart. Shell depends on. The . dmg image file will. Source. distribution. The. source code for martj is. GIT, but you will need the ant. All other JAR files which the. Java- based Bio. Mart applications depend on can be found in the lib. Downloading biomart- perl. There is no binary distribution for. It is only available as a source distribution. CVS. To check biomart- perl. CVS, you need to type the following commands on the command. The password you need to enter when asked is CVSUSER. For details on. how to configure it, please refer to the section on installing. Installing martj. You. need to have Java 1. You can get Java from. To do so requires you to. Registry file, which is discussed elsewhere in this. Running these scripts from other. Installing biomart- perl. Prerequisites. You. Perl version 5. 6. You can get. the latest version of Perl from http: //www. It is. important that you do not modify the directory structure inside the. Perl modules. When you run the configuration. URLPointer. xml. The. CPAN shell. Read the questions. CPAN asks during installation thoroughly, and answer yes. It is. usually fine to accept the default responses for almost all questions. For reference, the list of. CPAN modules required at the time of writing is shown below. This can be downloaded from. You do not. need to configure Apache to be used with Bio. Mart, as the Bio. Mart. configuration scripts will handle that for you. Mart. View works fine with all. Apache 1. 3 or higher, including Apache 2. Mart. View requires a few Apache. It does not matter if they are. Apache or provided as dynamic modules. If you are. missing any of them, the website where you can download them is. If you do not, then Mart. View is likely to be very slow. For Apache 2. 0 or higher, use. For Apache versions before 2. It. requires this tool to live in the same location as the Apache binary. If. you have installed a binary distribution of Apache, you may also need. Apache development tools to make apxs/apxs. Other Apache modules are also. Mart. View but these are all available with the default Apache. Apache and Mod. Perl quick setup. If you. do not already have Apache and Mod. Perl installed on your system then. For other operating systems, please refer to the Apache and. Mod. Perl websites for instructions. For. the purposes of these instructions it is assumed that you will be. Apache and Mod. Perl that were. Apache 2. 2. 1. 4 and Mod. Perl 2. 0. 4). It can use other versions if. First. you will need to create a directory where you can work. In our. example we will install Apache in /home/biomart/apache. Your Apache installation path is. You can use the same technique. Perl module. dependencies for biomart- perl. You will know if you need to. Apache error log that refer to. Apache/Response. cd /home/biomart/apache/sourcewget. When using the Perl API, this registry. Registry. files are in XML format. You will find a number of example registry. Change into the biomart- perl. URLPointer. xmlwhere registry. URLPointer. xml. is the registry file you wish to use from the conf. The first question the configure. Do you want to install in API only mode. If this happens, follow. Perl modules. When it has completed. Looks good.. Leaving it as localhost is fine for most cases. Mart. View should listen on for requests. The default one. should work fine. If Mart. View will be the only application served on. Mart. View via a web browser. If your server is receiving port forwarded requests from a. As Mart. View needs to encode the hostname. For the normal scenario of no. URL that will be used to access. Mart. View. The URL will be formed of the server name, followed by the. The. default setting on biomart will be used in all URL examples in this. Other optional settings can be. URLs from query results. It is possible to enable. The directory. settings and mail options are all configured here as well. Other. configurable options include how long session related data is stored. You may also like to edit the. Instructions for both settings. If this happens, follow. Perl modules. Mart. View will now proceed to. Registry file and download the various dataset. It will build templates for then. Mart. View website. This may take quite. The final message you see before completion should be: Compiling. Starting and stopping Mart. View. Change to. biomart- perldirectory. Apache/binary for the correct Apache location. Apache/binary - d $PWD - f. PWD/conf/httpd. conf. Test Mart. View by pointing your. URL, substituting < host>. This is potentially dangerous if you have. Apache instance running on your machine and so should. Therefore you should always be careful not to. Troubleshooting Mart. View startup. The following information may. Mart. View will not start up correctly. Thanks to. Eric Ross for providing most of it. Useless use of Allow. Override (in console)This is an Apache version issue. Couldn't determine Username (in console)Your operating system may not. Apache web browser process owner. It. can be resolved by adding User www. Also make sure the ownership of the biomart directory is www. If Apache runs under a different. No such file or directory (in the log)The martview, martresults. Perl. Reinstall mod. Reinstall mod. To do this you must first stop. Mart. View, then change to the biomart- perl directory and type. Registry. xml. with your actual Registry file, just as you did when first. Registry. xml. Answer n. API, and answer y. The dataset configurations that were downloaded. Finally, the various templates that define the. Mart. View pages will be rebuilt and recompiled to match any changes. You can now safely start Mart. View. up again. 1. Switching to a different Registry. If you alter the Registry file so. Registry file, then Mart. View needs to be reconfigured from. Registry. If you have renamed the registry. New. Registry. xml. If the altered registry still has. Registry. xml. 1. Changing memory usage. The default behaviour suitable. If memory is an issue then you can run configure. These options can. For example to. reconfigure the server in lazyload mode if none of the underlying. Registry. xml. 1. Clearing download files. An optional setting in the. Mart. View to request that their queries be run in the. Files can be removed safely just by. Clearing log files. Log files are kept in the log. The logs are written by Apache, and can be maintained in. Apache logs are maintained. In other words, you can. Make sure you do not accidentally. If you do so. it becomes harder to stop Mart.
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