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Installation notes for tRNAscan-SE version 2.0.9 (July 2021)
Home Page
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.
- $ sudo apt-get install infernal infernal-doc
Installation
- Move the old version, but keep in case we want it
$ mv /usr/local/bin/tRNAscan-SE{,.1.3.1}
- $ ver="2.0.9"
- $ cd /programinstallers/
- $ wget -N http://trna.ucsc.edu/software/trnascan-se-$ver.tar.gz
- $ tar -zxvf trnascan-se-$ver.tar.gz
- $ cd tRNAscan-SE-2.0
- $ ./configure --prefix=/usr/local/bin/tRNAscan-SE
- $ make
- $ sudo make install
- Add to PATH for all users
$ sudo nano /etc/profile
…
PATH="$PATH:/usr/local/bin/tRNAscan-SE/bin"
…
- Cleanup
$ cd /programinstallers
$ rm tRNAscan-SE-2.0 -rf
- Because Infernal is not installed alongside tRNAscan-SE
$ cd /usr/local/bin/tRNAscan-SE/bin
$ 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)
Home Page
Prerequisites
Perl5
Installation
- $ cd /programinstallers/
- $ wget -N http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
- $ tar -zxvf tRNAscan-SE.tar.gz
- $ cd tRNAscan-SE-1.3.1
- 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:
- where executables are to be installed
- where data files are to be installed
- where Perl is already installed on the system
- what the Perl binary is called (i.e. 'perl' or 'perl5')
- where temporary files will reside
- 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
- $ make
- $ 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
- Cleanup
$ cd ..
- $ rm tRNAscan-SE-1.3.1 -rf
- 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
- I also needed to do this (permissions were 754 previously)
$ sudo chmod 755 /usr/local/bin/tRNAscanSE
- 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