Configuring STARS on Bio-Linux
Setting the path
The phred and phrap program directories need to be added to your path before they can be used by STARS.
This can be achieved by editing the bioenvrc config file using a text editor (e.g. pico). The file locations are different depending on whether you are using Bio-Linux version 3 or 4.
Bio-Linux 3:
sudo pico -w /usr/software/bioenvrc
Towards the bottom of this file is a section that reads:
#########################################################
#UNCOMMENT THESE LINES IF YOU HAVE INSTALLED TRACE2DBEST#
#########################################################
#export PHRED_PARAMETER_FILE=/usr/software/phred/phred/phredpar.dat;
#export PATH=$PATH:/usr/software/blast/blast: /usr/software/netblast/netblast: /usr/software/phred/phred: /usr/software/phrap/phrap: /usr/sbin
Remove the '#' from the two export lines. Exit the editor (Ctrl-X) and save when prompted.
Changes to the path take affect from the next time you log in. Alternatively type:
source /usr/software/bioenvrc
for the changes to take immediately.
Bio-Linux 4:
sudo pico -w /usr/local/bioinf/config_files/customrc
Add the following lines at the bottom:
export PHRED_PARAMETER_FILE=/usr/local/bioinf/phred/phred/phredpar.dat;
export PATH=$PATH:/usr/software/phred/phred:/usr/software/phrap/phrap;
Changes to the path take affect from the next time you log in. Alternatively type:
source /usr/local/bioinf/config_files/bioenvrc
for the changes to take immediately.