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

Tue Nov 21 23:56:48 UTC 2006

On Nov 21, 2006, at 2:53 PM, Brian Osborne wrote:

> 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.

Agreed (thanks Brian for pointing that out).  I have to update these  
by hand until I can find a more automated way (which will be hard  
considering the meta content in the wiki).

Chris

>
>
>
> 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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> Bioperl-guts-l at lists.open-bio.org
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>
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>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign