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Installation notes for tRNAscan-SE version 2.0.9 (July 2021)

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Prerequisites

tRNAscan-SE 2.0 requires separate installation of Infernal 1.1.2. The source code and prebuilt binaries can be obtained at http://eddylab.org/infernal/.
The installation directory of Infernal should be the same as the one where tRNAscan-SE 2.0 is installed.

  1. $ sudo apt-get install infernal infernal-doc

Installation

  1. Move the old version, but keep in case we want it
    $ mv /usr/local/bin/tRNAscan-SE{,.1.3.1}
  2. $ ver="2.0.9"
  3. $ cd /programinstallers/
  4. $ wget -N http://trna.ucsc.edu/software/trnascan-se-$ver.tar.gz
  5. $ tar -zxvf trnascan-se-$ver.tar.gz
  6. $ cd tRNAscan-SE-2.0
  7. $ ./configure --prefix=/usr/local/bin/tRNAscan-SE
  8. $ make
  9. $ sudo make install
  10. Add to PATH for all users
    $ sudo nano /etc/profile

    PATH="$PATH:/usr/local/bin/tRNAscan-SE/bin"
  11. Cleanup
    $ cd /programinstallers
  12. $ rm tRNAscan-SE-2.0 -rf
  13. Because Infernal is not installed alongside tRNAscan-SE
    $ cd /usr/local/bin/tRNAscan-SE/bin
  14. $ for p in cmbuild cmcalibrate cmsearch cmscan smalign ; do sudo ln -s /usr/bin/$p ; done

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