[Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24
Chris Fields
cjfields at uiuc.edu
Tue Nov 21 18:56:48 EST 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
> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l
>
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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
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