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安装BioPerl for windows(Linux)  

2009-11-04 18:32:44|  分类: perl&bioperl |  标签: |举报 |字号 订阅

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原文:  http://www.bioperl.org/wiki/Installing_BioPerl   
     http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix 
   http://www.bioperl.org/wiki/Installing_BioPerl_on_Windows
CPAN是Comprehensive Perl Archive Network的缩写.。它是一个巨大的Perl软件收藏库,收集了大量有用的Perl模块(modules)及其相关的文件。在互联网上可在此URL([url]www.cpan.org[/url])找到CPAN。

Installation using CPAN or manual installation (WIN)

Installation using PPM is preferred since it is easier, but if you run into problems, or a PPM isn't available for the version/package of BioPerl you want, or you want to choose which optional dependencies to install, you can install manually by downloading the appropriate package or by using CPAN. In fact both methods ultimately need nmake to be installed, CPAN to be upgraded to >= v1.81, Module::Build to be installed (>= v0.2805) and Test::Harness to be upgraded to >= v2.62:

1) Download nmake
2) Double-click to run it, which extracts 3 files. Move both NMAKE.EXE and the NMAKE.ERR files to a place in your PATH; if set up properly, you can move these to your Perl bin directory, normally C:\Perl\bin.
1) Open a cmd window by going to Start >> Run and typing 'cmd' into the box and pressing return.
2) Type 'cpan' to enter the CPAN shell.
3) At the cpan> prompt, type 'install CPAN' to upgrade to the latest version.
4) Quit (by typing 'q') and reload cpan. You may be asked some configuration questions; accepting defaults is fine.
5) At the cpan> prompt, type 'o conf prefer_installer MB' to tell CPAN to prefer to use Build.PL scripts for installation. Type 'o conf commit' to save that choice.
6) At the cpan> prompt, type 'install Module::Build'.
7) At the cpan> prompt, type 'install Test::Harness'.

You can now follow the unix instructions for installing using CPAN, or install manually:

8) Download the .zip version of the package you want.
9) Extract the archive in the normal way.
10) In a cmd window 'cd' to the directory you extracted to. Eg. if you extracted to directory 'Temp', 'cd Temp\bioperl-1.5.2_100'
11) Type 'perl Build.PL' and answer the questions appropriately.
12) Type 'perl Build test'. All the tests should pass, but if they don't let us know. Your usage of BioPerl may not be affected by the failure, so you can choose to continue anyway.
13) Type 'perl Build install' to install BioPerl.


Installing using Build.PL(linux)

The advantage of this approach is it's stepwise, so it's easy to stop and analyze in case of any problem.

Download, then unpack the appropriate package. For example:

>tar xvfz BioPerl-1.6.1.tar.gz
>cd BioPerl-1.6.1

Now issue the build commands:

>perl Build.PL
>./Build test

If you've installed everything perfectly and all the network connections are working then you may pass all the tests run in the './Build test' phase. It's also possible that you may fail some tests. Possible explanations: problems with local Perl installation, network problems, previously undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that there are over 800 modules in Bioperl and the test suite is running more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl.

If you decide that the failed tests will not affect how you intend to use Bioperl and you'd like to install anyway, or if all tests were fine, do:

>./Build install

However, if you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org.

To './Build install' you need write permission in the perl5/site_perl/source area (or similar, depending on your environment). Usually this will require you becoming root, so you will want to talk to your systems manager if you don't have the necessary privileges.

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