求助,安装了一个linux下专用的生物学软件,不会运行

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cweiyu
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求助,安装了一个linux下专用的生物学软件,不会运行

#1

帖子 cweiyu » 2008-08-31 11:08

由于实验的需要下载了这个基因序列分析软件,只有linux版,按照install文件里的说明安装了

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
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xiaomao101
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#2

帖子 xiaomao101 » 2008-08-31 11:15

没用过,不过我会用google,看看这里网站能不能把帮助你启动你的软件
http://lodore.genetics.utah.edu/oaf/download
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xiaomao101
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#3

帖子 xiaomao101 » 2008-08-31 11:17

看了网站上的东西,貌似oaf.pl这个perl文件就是你的运行的主程序喽
$ ./oaf.pl + 你的数据
就行喽
cweiyu
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#4

帖子 cweiyu » 2008-09-09 20:14

xiaomao101 写了:看了网站上的东西,貌似oaf.pl这个perl文件就是你的运行的主程序喽
$ ./oaf.pl + 你的数据
就行喽
谢谢,研究很久还是不行,我再找找原因
技术?不懂……我就是跟着起哄的
所以我爱看pk版
xitoong
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Re: 求助,安装了一个linux下专用的生物学软件,不会运行

#5

帖子 xitoong » 2012-08-08 0:20

不知道楼主现在解决没? :em09
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