Configuring STARS on Bio-Linux
Installing phred
The distribution file should be named something like phred-dist-020425.c-acd.tar.Z. In the following instructions use the name of the file that you have received.
Make a temporary directory 'phred' and move the distribution file into it:
mkdir phred
mv phred-dist-020425.c-acd.tar.Z phred
cd phred
You now need to uncompress the file:
uncompress phred-dist-020425.c-acd.tar.Z
tar xvf phred-dist-020425.c-acd.tar
To compile the program with the correct optimisations, you will need to edit one line in the 'Makefile' file. Using the pico text editor (type 'pico Makefile'), remove the '#' from the beginning of the line that reads:
LXFLAGS = -DX86_GCC_LINUX
exit the editor (Ctrl-X) and save when prompted. To compile the program type:
make
Copy the newly created executable file 'phred' to /usr/software/phred (use the version number of the file you have been sent):
sudo mkdir -p /usr/software/phred/phred_020425
sudo ln -s /usr/software/phred/phred_020425 /usr/software/phred/phred
sudo cp phred /usr/software/phred/phred
sudo chmod go-r /usr/software/phred/phred/phred
Copy the phredpar.dat file to /usr/software/phred/phred:
sudo cp phredpar.dat /usr/software/phred/phred