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Chris Fields committed Mar 1, 2012
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18 changes: 9 additions & 9 deletions INSTALL
@@ -1,4 +1,4 @@
Installing BioPerl for Unix
Installing BioPerl for Unix

* 1 BIOPERL INSTALLATION
* 2 SYSTEM REQUIREMENTS
Expand Down Expand Up @@ -144,7 +144,7 @@ INSTALLING BIOPERL THE EASY WAY USING CPAN
You can use the CPAN shell to install BioPerl. For example:

>perl -MCPAN -e shell

Or you might have the cpan alias installed:

>cpan
Expand All @@ -155,9 +155,9 @@ Then find the name of the BioPerl version you want:
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 C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Expand Down Expand Up @@ -193,7 +193,7 @@ Previously, 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.
Build.PL installation process discussed above.

EXTERNAL PROGRAMS

Expand All @@ -206,7 +206,7 @@ all the programs in the EMBOSS suite (Bio::Factory::EMBOSS). Most
of the modules which 'wrap' these programs are located in the separate
bioperl-run distribution; however, two commonly-used modules are still
distributed with the BioPerl core (Bio::Tools::Run::StandAloneBlast,
Bio::Tools::Run::RemoteBlast).
Bio::Tools::Run::RemoteBlast).

Environment Variables

Expand Down Expand Up @@ -279,7 +279,7 @@ 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
Expand Down Expand Up @@ -383,12 +383,12 @@ 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).
later).

For the 1.6 release and beyond, tests have been organized into groups
based upon the specific task or class the module being tested belongs
to. If you want to investigate the behavior of a specific test such as
the Seq test you would type:
the Seq test you would type:

>./Build test --test_files t/Seq/Seq.t --verbose

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