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预测tRNA的软件tRNAscan-SE的 安装

2024-07-08 12:29:28   224人阅读

Carrot root and DNAVCRU BioinformaticsUSDA ARS Vegetable Crops Research Unit

This page was last updated on Wednesday, 22-Jan-2014 16:11:26 CST

Installation notes for tRNAscan-SE version 1.3.1 (January 2012)

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Prerequisites

Perl5

 

Installation

    1. $ cd /programinstallers/
    2. $ wget -N http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
    3. $ tar -zxvf tRNAscan-SE.tar.gz
    4. $ cd tRNAscan-SE-1.3.1
    5. Edit the top of the Makefile.
      $ nano Makefile
      Set the paths and other make variables to suit your system.
      In particular, you need to specify:
      1. where executables are to be installed
      2. where data files are to be installed
      3. where Perl is already installed on the system
      4. what the Perl binary is called (i.e. ‘perl‘ or ‘perl5‘)
      5. where temporary files will reside
      6. where to install man pages
      PERLDIR = /usr/bin
      PERLBIN = perl
      BINDIR  = $(HOME)/bin
      LIBDIR  = $(HOME)/lib/tRNAscan-SE
      MANDIR  = $(HOME)/man
      TEMPDIR = /tmp
      becomes
      PERLDIR = /usr/bin
      PERLBIN = perl
      BINDIR  = /usr/local/bin
      LIBDIR  = /usr/local/lib/tRNAscan-SE
      MANDIR  = /usr/local/share/man
      TEMPDIR = /tmp
    6. $ make
    7. $ sudo make install
      .
      .
      .
      cp trnascan-1.4 covels-SE coves-SE eufindtRNA tRNAscan-SE /usr/local/bin/.
      cp -R tRNAscanSE /usr/local/bin/
      cp TPCsignal Dsignal *.cm gcode.* /usr/local/lib/tRNAscan-SE/.
      cp tRNAscan-SE.man /usr/local/share/man/man1/tRNAscan-SE.1
    8. Cleanup
      $ cd ..
    9. $ rm tRNAscan-SE-1.3.1 -rf
    10. To correct the error message
      Can‘t locate tRNAscanSE/Utils.pm in @INC (@INC contains:...
      I patched /usr/local/bin/tRNAscan-SE with the following additional line
      use lib "/usr/local/bin"; # otherwise can‘t find modules listed below
      inserted at line 28
    11. I also needed to do this (permissions were 754 previously)
      $ sudo chmod 755 /usr/local/bin/tRNAscanSE
    12. And for cgi compatibility, found three system() calls to rm in /usr/local/bin/tRNAscan-SE, changed to use the full path for each of these/bin/rm                  
    13. 转载于：http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/trnascan-se.htm


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