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final documentation revisions

svn path=/bioperl-live/branches/branch-1-5-2/; revision=11042
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Showing with 199 additions and 65 deletions.
  1. +9 −5 DEPENDENCIES
  2. +67 −21 INSTALL
  3. +123 −39 INSTALL.WIN
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14 DEPENDENCIES
@@ -1,15 +1,19 @@
-# $Id: DEPENDENCIES,v 1.1.2.3 2006-11-23 12:36:14 sendu Exp $
+# $Id: DEPENDENCIES,v 1.1.2.4 2006-12-06 18:20:16 sendu Exp $
BioPerl Dependencies
-The following packages are used by Bioperl. Not all are required for
-Bioperl to operate properly, however some functionality will be missing
-without them. You can easily install all of these during the normal
-installation process.
+The following packages are used by BioPerl. Not all are required for
+BioPerl to operate properly, however some functionality will be missing
+without them. You can easily choose to install all of these during the
+normal installation process. Note that the PPM version of the BioPerl
+packages always tries to install all dependencies.
The DBD::mysql, DB_File and XML::Parser modules require other applications
or databases: MySQL, Berkeley DB, and expat respectively.
+NB: This list of packages is not authoritative. See the 'requires',
+'build_requires' and 'recommends' sections of Build.PL instead.
+
+-----------------------------------------------------------------------------+
| Module | Where it is Used | Bio* Modules Affected |
|----------------------+-----------------------+------------------------------+
View
88 INSTALL
@@ -2,24 +2,28 @@
Installing Bioperl for Unix
- * BIOPERL INSTALLATION
- * SYSTEM REQUIREMENTS
- * OPTIONAL
- * ADDITIONAL INSTALLATION INFORMATION
- * THE BIOPERL BUNDLE
- * INSTALLING BIOPERL THE EASY WAY USING CPAN
- * INSTALLING BIOPERL THE EASY WAY USING Build.PL
- * WHERE ARE THE MAN PAGES?
- * EXTERNAL PROGRAMS
- * Environment Variables
- * INSTALLING BIOPERL SCRIPTS
- * INSTALLING BIOPERL IN A PERSONAL MODULE AREA
- * INSTALLING BIOPERL MODULES THE HARD WAY
- * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION
- * THE TEST SYSTEM
- * BUILDING THE OPTIONAL bioperl-ext PACKAGE
- * CONFIGURING for BSD and Solaris boxes
- * INSTALLATION
+ * 1 BIOPERL INSTALLATION
+ * 2 SYSTEM REQUIREMENTS
+ * 3 OPTIONAL
+ * 4 ADDITIONAL INSTALLATION INFORMATION
+ * 5 THE BIOPERL BUNDLE
+ * 6 PRELIMINARY PREPARATION
+ * 7 INSTALLING BIOPERL THE EASY WAY USING CPAN
+ * 8 INSTALLING BIOPERL THE EASY WAY USING 'Build.PL'
+ * 9 WHERE ARE THE MAN PAGES?
+ * 10 EXTERNAL PROGRAMS
+
+ * 10.1 Environment Variables
+
+ * 11 INSTALLING BIOPERL SCRIPTS
+ * 12 INSTALLING BIOPERL IN A PERSONAL MODULE AREA
+ * 13 INSTALLING BIOPERL MODULES THE HARD WAY
+ * 14 USING MODULES NOT INSTALLED IN THE STANDARD LOCATION
+ * 15 THE TEST SYSTEM
+ * 16 BUILDING THE OPTIONAL bioperl-ext PACKAGE
+
+ * 16.1 CONFIGURING for BSD and Solaris boxes
+ * 16.2 INSTALLATION
BIOPERL INSTALLATION
@@ -51,6 +55,7 @@ ADDITIONAL INSTALLATION INFORMATION
* Additional information on Bioperl and MAC OS:
* OS 9 - http://bioperl.org/Core/mac-bioperl.html
* OS X - http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html
+ (outdated, but useful for libgd installation notes)
* OS X - Installing using Fink (in Getting BioPerl)
THE BIOPERL BUNDLE
@@ -60,6 +65,42 @@ You no longer need to install Bundle::BioPerl. Instead, the normal
installation process will ask you if you'd like to install the
optional external module dependencies that Bioperl has.
+A full list of BioPerl dependencies can be found inf the DEPENDENCIES
+file included with this distribution.
+
+PRELIMINARY PREPARATION
+
+ This is optional, but regardless of your subsequent choice of installation
+ method, it will help to carry out the following steps. They will increase
+ the likelyhood of installation success (especially of optional
+ dependencies).
+
+ * Upgrade CPAN:
+
+ >perl -MCPAN -e shell
+ cpan>install Bundle::CPAN
+ cpan>q
+
+ * Install/upgrade Module::Build, and make it your preferred installer:
+
+ >cpan
+ cpan>install Module::Build
+ cpan>o conf prefer_installer MB
+ cpan>o conf commit
+ cpan>q
+
+ * Install the expat and libgd libraries by whatever method is
+ appropriate for your system. If you install libgd in a non-standard
+ location, that is fine: when installing the perl module that needs it
+ you will be asked where you installed it.
+
+ * If your expat library is installed in a non-standard location, tell
+ CPAN about it:
+
+ >cpan
+ cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include"
+ cpan>o conf commit
+
INSTALLING BIOPERL THE EASY WAY USING CPAN
You can use the CPAN shell to install Bioperl. For example:
@@ -220,9 +261,11 @@ INSTALLING BIOPERL SCRIPTS
Bioperl comes with a set of production-quality scripts that are
kept in the scripts/ directory. You can install these scripts if you'd
like, simply answer the questions during 'perl Build.PL'.
-The installation directory can be specified by
+The installation directory can be specified by:
+
perl Build.PL
./Build install --install_path script=/foo/scripts
+
By default they install to /usr/bin or similar, depending on platform.
INSTALLING BIOPERL IN A PERSONAL MODULE AREA
@@ -356,8 +399,11 @@ Smith-Waterman, Bio::Tools::dpAlign for protein Smith-Waterman,
Bio::SearchDist for EVD fitting of extreme value,
Bio::SeqIO::staden).
-This Installation works out-of-the box for all platforms except BSD
-and Solaris boxes. For other platforms skip this next paragraph.
+This Installation may work out-of-the box for most platforms except BSD
+and Solaris boxes. For other platforms skip this next paragraph. Of note,
+the code for bioperl-ext has not been updated along with the rest of bioperl,
+so one may expect to see some issues. If so, please report them to the
+BioPerl mailing list.
CONFIGURING for BSD and Solaris boxes
View
162 INSTALL.WIN
@@ -1,4 +1,4 @@
-# $Id: INSTALL.WIN,v 1.20.4.4 2006-11-21 10:33:26 sendu Exp $
+# $Id: INSTALL.WIN,v 1.20.4.5 2006-12-06 18:20:16 sendu Exp $
Installing Bioperl on Windows
@@ -6,23 +6,28 @@
* 1 Introduction
* 2 Requirements
- * 3 Installation Guide
- * 4 Bioperl
- * 5 Perl on Windows
- * 6 Bioperl on Windows
- * 7 Beyond the Core
-
- * 7.1 Setting environment variables
- * 7.2 Installing bioperl-db
-
- * 8 Bioperl in Cygwin
- * 9 bioperl-db in Cygwin
- * 10 Cygwin tips
- * 11 MySQL and DBD::mysql
- * 12 Expat
- * 13 Directory for temporary files
- * 14 BLAST
- * 15 Compiling C code
+ * 3 Installation using the Perl Package Manager
+
+ * 3.1 GUI Installation
+ * 3.2 Comand-line Installation
+
+ * 4 Installation using CPAN or manual installation
+ * 5 Bioperl
+ * 6 Perl on Windows
+ * 7 Bioperl on Windows
+ * 8 Beyond the Core
+
+ * 8.1 Setting environment variables
+ * 8.2 Installing bioperl-db
+
+ * 9 Bioperl in Cygwin
+ * 10 bioperl-db in Cygwin
+ * 11 Cygwin tips
+ * 12 MySQL and DBD::mysql
+ * 13 Expat
+ * 14 Directory for temporary files
+ * 15 BLAST
+ * 16 Compiling C code
Introduction
@@ -39,8 +44,8 @@ Introduction
Requirements
- 1) Only ActivePerl >= 5.8.8.819 is supported by the Bioperl team.
- Earlier versions may work, but we do not support them.
+ Only ActivePerl >= 5.8.8.819 is supported by the Bioperl team. Earlier
+ versions may work, but we do not support them.
One of the reason for this requirement is that ActivePerl >= 5.8.8.819 now
use Perl Package Manager 4 (PPM4). PPM4 is now superior to earlier
@@ -49,43 +54,121 @@ Requirements
PPM and also easier for you to do the install! Proceed with earlier
versions at your own risk.
-Installation Guide
+ To install ActivePerl:
1) Download the ActivePerl MSI from ActiveState
2) Run the ActivePerl Installer (accepting all defaults is fine).
- 3) Start the Perl Package Manager GUI from the Start menu.
+Installation using the Perl Package Manager
+
+ GUI Installation
- 4) Go to Edit >> Preferences and click the Repositories tab. Add a
+ 1) Start the Perl Package Manager GUI from the Start menu.
+
+ 2) Go to Edit >> Preferences and click the Repositories tab. Add a
new repository for each of the following:
Repositories to add
+----------------------------------------------------------------+
| Name | Location |
|--------------------------+-------------------------------------|
- |BioPerl-Release Candidates| http://bioperl.org/DIST/RC |
+ |BioPerl-Release Candidates|[37]http://bioperl.org/DIST/RC |
|--------------------------+-------------------------------------|
- |BioPerl-Regular Releases | http://bioperl.org/DIST |
+ |BioPerl-Regular Releases |[38]http://bioperl.org/DIST |
|--------------------------+-------------------------------------|
- |Kobes | http://theoryx5.uwinnipeg.ca/ppms|
+ |Kobes |[39]http://theoryx5.uwinnipeg.ca/ppms|
|--------------------------+-------------------------------------|
- |Bribes | http://www.Bribes.org/perl/ppm |
+ |Bribes |[40]http://www.Bribes.org/perl/ppm |
+----------------------------------------------------------------+
- 5) Select View >> All Packages.
+ 3) Select View >> All Packages.
+
+ 4) In the search box type bioperl.
- 6) In the search box type bioperl.
+ 5) Right click the latest version of Bioperl available and choose
+ install.
- 7) Right click the latest version of Bioperl available and choose
- install. (Note for users of previous Bioperl releases: you should
- not have to use the Bundle-BioPerl package anymore.)
+ 5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will
+ be marked for installation. If you see that some of them complain
+ about needing a command-line installation (eg. XML::SAX::ExpatXS),
+ and you want those particular pre-requisites, stop now (skip step
+ 6) and see the 'Command-line Installation' section.
- 8) Click the green arrow (Run marked actions) to complete the
+ 6) Click the green arrow (Run marked actions) to complete the
installation.
- 9) Go to the Bioperl Wiki and start reading documentation.
+ Comand-line Installation
+
+ 1) Follow steps 1) and 2) from 'GUI Installation' above, if you
+ haven't done so already.
+
+ 2) Open a cmd window by going to Start >> Run and typing 'cmd' and
+ pressing return.
+
+ 3) Type the following into the cmd window:
+
+ ppm-shell
+ search bioperl
+ install #
+
+ (where the number matches the bioperl version needed) You can use '-force'
+ to force install if needed.
+
+Installation using CPAN or manual installation
+
+ 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.
Bioperl
@@ -151,9 +234,9 @@ Perl on Windows
most common and easiest is to get the most recent build from
ActiveState, a software company that provides free builds of Perl for
Windows users. The current (October 2006) build is ActivePerl 5.8.8.819.
- Bioperl also works on Perl 5.6.x but due to installation problems etc,
- only ActivePerl 5.8.8.819 or later is supported. To install ActivePerl on
- Windows:
+ Bioperl also works on Perl 5.6.x, but due to installation problems etc,
+ only ActivePerl 5.8.8.819 or later is supported for WinXP installation.
+ To install ActivePerl on Windows:
1) Download the ActivePerl MSI from
http://www.activestate.com/Products/ActivePerl/.
@@ -320,7 +403,7 @@ Beyond the Core
regular bioperl 1.5.2 release PPM. We will post instructions at that
time on using PPM to install bioperl-db.
- to begin, follow instructions detailed in the Installation Guide for
+ To begin, follow instructions detailed in the Installation Guide for
adding the three new repositories (Bioperl, Kobes and Bribes). Then
install the following packages:
@@ -426,7 +509,8 @@ Beyond the Core
Bioperl in Cygwin
Cygwin is a Unix emulator and shell environment available free at
- http://www.cygwin.com. Bioperl v. 1.* runs well within Cygwin. Some
+ http://www.cygwin.com. Bioperl v. 1.* supposedly runs well within Cygwin,
+ though the latest release has not been tested with Cygwin yet. Some
users claim that installation of Bioperl is easier within Cygwin than
within Windows, but these may be users with UNIX backgrounds. A note on
Cygwin: it doesn't write to your Registry, it doesn't alter your system or
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