[Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24

Brian Osborne bosborne11 at verizon.net
Tue Nov 21 15:53:39 EST 2006


Bioperl-l,

INSTALL has changed in CVS but the Wiki's version has not - you always have
to change both versions of the INSTALL instructions, this is how Chris has
elected to do it.

Brian O.



Date: Tue, 21 Nov 2006 10:32:36 +0000
To: <bioperl-guts-l at bioperl.org>
Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57,
1.58 INSTALL.WIN, 1.23, 1.24

Update of /home/repository/bioperl/bioperl-live
In directory dev.open-bio.org:/tmp/cvs-serv14112

Modified Files:
 DEPENDENCIES INSTALL INSTALL.WIN
Log Message:
clarification for Bundle::BioPerl, updates for Build.PL

Index: DEPENDENCIES
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1
--- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2
***************
*** 5,10 ****
  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, except srsperl.pm,
! using the Bundle::BioPerl CPAN bundle.
  
  The DBD::mysql, DB_File and XML::Parser modules require other applications
--- 5,11 ----
  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 by using CPAN to install
! Bioperl, or if you have installed Bioperl manually (from archive or CVS),
! by using the Bundle::BioPerl CPAN bundle.
  
  The DBD::mysql, DB_File and XML::Parser modules require other applications

Index: INSTALL
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v
retrieving revision 1.57
retrieving revision 1.58
diff -C2 -d -r1.57 -r1.58
*** INSTALL 16 Nov 2006 16:27:49 -0000 1.57
--- INSTALL 21 Nov 2006 10:32:34 -0000 1.58
***************
*** 1,24 ****
  # $Id$
  
!                           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 GNU 'make'
!      *  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
  
  BIOPERL INSTALLATION
--- 1,24 ----
  # $Id$
  
! 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
  
  BIOPERL INSTALLATION
***************
*** 41,48 ****
        modules is included in the DEPENDENCIES file.
  
! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of these
! external modules easy. Simply install the bundle using your CPAN shell and
! all necessary modules will be installed. See THE BIOPERL BUNDLE,
! below.
  
  OPTIONAL
--- 41,49 ----
        modules is included in the DEPENDENCIES file.
  
! When not using CPAN to install Bioperl itself, the CPAN Bioperl Bundle
! (Bundle::BioPerl) makes installation of these external modules easy.
Simply
! install the bundle using your CPAN shell and many optional modules will be
! installed. See THE BIOPERL BUNDLE, below. However, it is recommended you
use
! CPAN to install Bioperl and not use Bundle::BioPerl.
  
  OPTIONAL
***************
*** 61,64 ****
--- 62,72 ----
  THE BIOPERL BUNDLE
  
+ You do not need to install Bundle::BioPerl if you will install Bioperl
+ using CPAN. This is for users manually installing Bioperl from archives
+ or CVS, who also want an easy way to install the optional external
+ modules that Bioperl makes use of.
+ 
+ Bundle::BioPerl does *not* install Bioperl.
+ 
  You typically need root privileges to install using CPAN. If you don't
  have these privileges please see INSTALLING BIOPERL IN A PERSONAL
***************
*** 86,96 ****
   CPAN: Storable loaded ok
   Going to read /home/bosborne/.cpan/Metadata
!  Database was generated on Tue, 24 Feb 2004 23:55:23 GMT
!  DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz
!  DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz
  
  Now install:
  
!  cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz
  
  If you've installed everything perfectly and all the network connections
--- 94,105 ----
   CPAN: Storable loaded ok
   Going to read /home/bosborne/.cpan/Metadata
!  Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
!  Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz
!  Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz
!  Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz
  
  Now install:
  
!  cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
  
  If you've installed everything perfectly and all the network connections
***************
*** 100,105 ****
  undetected bug in Bioperl, flawed test script, problems with CGI
  script used for sequence retrieval at public database, and so on. Remember
! that there are over 700 modules in Bioperl and the test suite is running
! more than 9000 individual tests, a few failed tests may not affect your
  usage of Bioperl.
  
--- 109,114 ----
  undetected bug in Bioperl, flawed test script, problems with CGI
  script used 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.
  
***************
*** 107,111 ****
  Bioperl and you'd like to install anyway do:
  
!  cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz
  
  This is what most experienced Bioperl users would do. However, if you're
--- 116,120 ----
  Bioperl and you'd like to install anyway do:
  
!  cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
  
  This is what most experienced Bioperl users would do. However, if you're
***************
*** 113,117 ****
  bioperl-l at bioperl.org.
  
! INSTALLING BIOPERL THE EASY WAY USING GNU 'make'
  
  The advantage of this approach is it's stepwise, so it's easy to stop and
--- 122,126 ----
  bioperl-l at bioperl.org.
  
! INSTALLING BIOPERL THE EASY WAY USING Build.PL
  
  The advantage of this approach is it's stepwise, so it's easy to stop and
***************
*** 120,126 ****
  Download, then unpack the tar file. For example:
  
!  >gunzip bioperl-1.5.2.tar.gz
!  >tar xvf bioperl-1.5.2.tar
!  >cd bioperl-1.5.2
  
  Now issue the make commands:
--- 129,135 ----
  Download, then unpack the tar file. For example:
  
!  >gunzip bioperl-1.5.2_100.tar.gz
!  >tar xvf bioperl-1.5.2_100.tar
!  >cd bioperl-1.5.2_100
  
  Now issue the make commands:
***************
*** 135,141 ****
  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 700 modules in Bioperl and the test suite is running almost
! 9000 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
--- 144,150 ----
  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
***************
*** 148,154 ****
  bioperl-l at bioperl.org.
  
! To 'make install' you need write permission in the perl5/site_perl/source
! area. 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.
  
  It is also straightforward to install the package outside of the this
--- 157,164 ----
  bioperl-l at 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.
  
  It is also straightforward to install the package outside of the this
***************
*** 158,165 ****
  WHERE ARE THE MAN PAGES?
  
! When using Makefile.PL, we had to disable the automatic creation of man
! pages because this step was triggering a "line too long" error on some
! OSs due to shell constraints. If you want man pages installed use the
! Build.PL installation process.
  
  EXTERNAL PROGRAMS
--- 168,176 ----
  WHERE ARE THE MAN PAGES?
  
! When using Makefile.PL (no longer covered in this documentation), we had
! to disable the automatic creation of man pages because this step was
! triggering a "line too long" error on some OSs due to shell constraints.
! If you want man pages installed use the Build.PL installation process
! discussed above.
  
  EXTERNAL PROGRAMS
***************
*** 229,234 ****
  like, simply answer the questions on 'perl Build.PL'.
  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.
  
--- 240,245 ----
  like, simply answer the questions on 'perl Build.PL'.
  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.
  
***************
*** 297,301 ****
  execute the make commands from the Compile/SW directory.
  
! If all else fails or are unable to access the perl distribution
  directories, ask your system administrator to place the files there for
  you. You can always execute perl scripts in the same directory as the
--- 308,312 ----
  execute the make commands from the Compile/SW directory.
  
! If all else fails and you are unable to access the perl distribution
  directories, ask your system administrator to place the files there for
  you. You can always execute perl scripts in the same directory as the
***************
*** 312,316 ****
   #!/usr/bin/perl
   use lib "/home/users/dag/lib/perl5/";
!  use Bio::Seq;
   #<...insert whizzy perl code here...>
  
--- 323,327 ----
   #!/usr/bin/perl
   use lib "/home/users/dag/lib/perl5/";
!  use Bio::Perl;
   #<...insert whizzy perl code here...>
  
***************
*** 319,341 ****
     csh or tcsh:
  
!  setenv PERL5LIB /home/users/dag/lib/perl5//
  
     bash or sh:
  
!  export PERL5LIB=/home/users/dag/lib/perl5//
  
  THE TEST SYSTEM
  
  The Bioperl test system is located in the t/ directory and is
! automatically run whenever you execute the 'make test' command.
  Alternatively if you want to investigate the behavior of a specific test
! such as the SeqIO test you would type:
  
!  >perl -I. -w t/SeqIO.t
  
! The -I. tells Perl to use the current directory as the include path - this
! makes sure you are testing the modules in this directory not ones
! installed elsewhere in your PERL5LIB path. The -w tells Perl to print all
! warnings.
  
  If you are trying to learn how to use a module, often the test suite is a
--- 330,357 ----
     csh or tcsh:
  
!  setenv PERL5LIB /home/users/dag/lib/perl5/
  
     bash or sh:
  
!  export PERL5LIB=/home/users/dag/lib/perl5/
  
  THE TEST SYSTEM
  
  The Bioperl test system is located in the t/ directory and is
! automatically run whenever you execute the './Build test' command
! (having previously run 'Perl Build.PL'; if you have already installed
! Bioperl answer 'no' to script installation to get nicer test output
! later).
  Alternatively if you want to investigate the behavior of a specific test
! such as the Seq test you would type:
  
!  >./Build test --test_files t/Seq.t --verbose
  
! The ./ ensures you are using the Build script in the current directory to
! make sure you are testing the modules in this directory not ones
! installed elsewhere. The --test_files arguement can be used multiple times
! to try a set of test scripts in one go. The --verbose arguement outputs
! the detailed test results, instead of just the summary you see during
! './Build test'.
  
  If you are trying to learn how to use a module, often the test suite is a
***************
*** 385,388 ****
  This should install the compiled extension. The Bio::Tools::pSW
  module will work cleanly now.
- 
-        
\ No newline at end of file
--- 401,402 ----

Index: INSTALL.WIN
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23
--- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24
***************
*** 80,89 ****
  
             7) Right click the latest version of Bioperl available and
choose
!            install.
! 
!                         7a) This package will be sufficient for the main
!                         functionality of Bioperl. However, if you require
!                         full functionality, you should also install the
!                         latest Bundle-BioPerl package.
  
             8) Click the green arrow (Run marked actions) to complete the
--- 80,85 ----
  
             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.)
  
             8) Click the green arrow (Run marked actions) to complete the

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