代码： 全选
# $Id: INSTALL,v 1.0.6 2008/01/25 02:53:11 Europe/Dublin $
o INSTALLATION
o SYSTEM REQUIREMENTS
o INSTALLING OAF
o INSTALLATION
Ornitine decarboxylase Antizyme Finder (OAF) has been installed
on many forms of Unix, MacOS X and probably on Win9X/NT/2000/XP.
o SYSTEM REQUIREMENTS
- perl 5.005 or later.
- Bioperl modules: OAF uses functionality provided
in Bioperl modules. (see http://www.bioperl.org/)
- HMMER is mandatory since OAF is base on HMM profiles.
(see http://hmmer.janelia.org/)
- FASTA is mandatory if you plan to use sequence longer than 20 kb.
(see ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/)
- BLAST is mandatory if you plan to search through a database,
except if you use the NCBI remote BLAST server.
(see http://www.ncbi.nlm.nih.gov/BLAST/download.shtml)
After installing HMMER, FASTA and BLAST packages on your system,
you may edit the environmental variable $HMMERDIR, $FASTADIR and
$BLASTDIR or your $PATH variable to point to the HMMER, FASTA and
BLAST directories repectively. Ensure that users have execute
privileges for those programs.
o INSTALLING OAF
The advantage of this approach is it's stepwise, so
it's easy to stop and analyse in case of any problem.
Download, then unpack the tar file. For example:
bunzip2 oaf-1.0.6.tar.bz2
tar xvf oaf-1.0.6.tar
cd oaf-1.0.6
Now issue the make commands:
perl Makefile.PL
make
sudo make install
To 'make install' you need write permission in the perl5/site_perl/
source area. Quite often this will require you becoming root, so
you will want to talk to your systems manager if you don't have
the necessary privileges.安装后的终端提示如下：
代码： 全选
cweiyu@cweiyu-laptop:~/桌面/oaf/oaf-1.0.6$ perl Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for Bio
cweiyu@cweiyu-laptop:~/桌面/oaf/oaf-1.0.6$ make
cp Bio/Tools/oaz.fs.hmm blib/lib/Bio/Tools/oaz.fs.hmm
cp Bio/Tools/oaz.hmm blib/lib/Bio/Tools/oaz.hmm
cp Bio/Tools/BlastTools.pm blib/lib/Bio/Tools/BlastTools.pm
cp Bio/Tools/BlastLocalTools.pm blib/lib/Bio/Tools/BlastLocalTools.pm
cp Bio/Tools/Run/StandAloneBlast.pm blib/lib/Bio/Tools/Run/StandAloneBlast.pm
cp Bio/Tools/OAF.pm blib/lib/Bio/Tools/OAF.pm
cp Bio/SearchIO/blastxml.pm blib/lib/Bio/SearchIO/blastxml.pm
cp Bio/Tools/oaz.fasta blib/lib/Bio/Tools/oaz.fasta
cp Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm
cp Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm
Manifying blib/man3/Bio::Tools::OAF.3pm
Manifying blib/man3/Bio::SearchIO::blastxml.3pm
Manifying blib/man3/Bio::Tools::BlastLocalTools.3pm
Manifying blib/man3/Bio::Tools::BlastTools.3pm
Manifying blib/man3/Bio::Tools::HMMER::Results.3pm
Manifying blib/man3/Bio::SearchIO::blast.3pm
Manifying blib/man3/Bio::Tools::Run::StandAloneBlast.3pm
cweiyu@cweiyu-laptop:~/桌面/oaf/oaf-1.0.6$ sudo make install
Installing /usr/local/share/perl/5.8.8/Bio/Tools/OAF.pm
Installing /usr/local/man/man3/Bio::Tools::BlastTools.3pm
Installing /usr/local/man/man3/Bio::Tools::OAF.3pm
Installing /usr/local/man/man3/Bio::Tools::HMMER::Results.3pm
Installing /usr/local/man/man3/Bio::Tools::BlastLocalTools.3pm
Installing /usr/local/man/man3/Bio::SearchIO::blastxml.3pm
Installing /usr/local/man/man3/Bio::SearchIO::blast.3pm
Installing /usr/local/man/man3/Bio::Tools::Run::StandAloneBlast.3pm
Writing /usr/local/lib/perl/5.8.8/auto/Bio/.packlist
Appending installation info to /usr/local/lib/perl/5.8.8/perllocal.pod
cweiyu@cweiyu-laptop:~/桌面/oaf/oaf-1.0.6$ 安装后在~/桌面/oaf/oaf-1.0.4$ 文件夹下生成了一些.pm文件，请问这种文件是不是软件运行的文件，应该怎么运行？
谢谢
