预测tRNA的软件tRNAscan-SE的 安装
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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)
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
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
- 转载于：http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/trnascan-se.htm
- 安装最主要的需要注意修改/usr/local/bin/tRNAscan-SE 中use lib "/usr/local/bin";的添加
