Tags
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
http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/trnascan-se.htm
http://gif.biotech.iastate.edu/Tutorial/doku.php?id=errors:snoscan_error