tRNAscan-SE | iAmphioxus

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For tRNAscan:

wget http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
tar -zxvf tRNAscan-SE.tar.gz
ln -s tRNAscan-SE-1.3.1 tRNAscan-SE
cd tRNAscan-SE

we might need to edit the Makefile if we want to customize the installation directory, here I used emacs for this:

 emacs Makefile

I modified the following lines from:

BINDIR = $(HOME)/bin
LIBDIR = $(HOME)/lib/tRNAscan-SE
MANDIR = $(HOME)/man

to:

BINDIR = $(HOME)/local/bin
LIBDIR = $(HOME)/local/lib/tRNAscan-SE
MANDIR = $(HOME)/local/share/man

Then, we are ready to compile the program.

make
make install
chmod 755 ~/local/bin/tRNAscan-SE

When running tRNAscan-SE, I got the following error message:
“Can’t locate tRNAscanSE/Utils.pm in @INC (@INC contains:…”

So we need to patch the following line in ~/local/bin/tRNAscan-SE at line 28 so that tRNAscan-SE can find the modules that it needs.

use lib "/home/<my_userid>/local/bin";

For snocan:

wget http://lowelab.ucsc.edu/snoRNAdb/code/snoscan-0.9b.tar.Z
tar xvzf snoscan-0.9b.tar.Z
ln -s snoscan-0.9b snoscan
cd snoscan

According to the README file, we need to compile squid-1.5j first, so

cd squid-1.5j

Again, we can customize the installation path like we did for tRNAscan-SE:

SQUIDHOME = $(HOME)/local/lib/squid
BINDIR = $(HOME)/local/bin
SCRIPTDIR = $(HOME)/local/scripts
MANDIR = $(HOME)/local/share/man

There is a type conflict in the original Makefile of squid-1.5j, so we need to do this:

sed -i 's/getline/getLine/g' sqio.c

then we can compile squid-1.5j:

make

Switch back to the directory of snocan, and modify the Makefile to set the installation path

cd ..
emacs Makefile

BINDIR = $(HOME)/local/bin
MANDIR = $(HOME)/local/share/man

make
make install

References

iAmphioxus