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Question: How do I get the path of the directory in which a  Bash  script is located FROM that Bash script? Answer: DIR = "$( cd " $ ( dirname "${BASH_SOURCE[0]}" ) " && pwd )" is a useful one-liner which will give you the full directory name of the script no matter where it is being called from. This will work as long as the last component of the path used to find the script is not a symlink (directory links are OK). If you want to also resolve any links to the script itself, you need a multi-line solution: SOURCE = "${BASH_SOURCE[0]}" while [ - h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink DIR = "$( cd -P " $ ( dirname "$SOURCE" ) " && pwd )" SOURCE = "$(readlink " $SOURCE ")" [[ $SOURCE != /* ]] && SOURCE = "$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative ...

Tip: Do NOT need to move SICER anymore. For SICER, if you are going to the original code, you have to copy the source code to your working directory. This is because the PATHTO variable varies when you’re doing different work. To avoid this, you can modify the code to: PATHTO="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" #SICER=$PATHTO/SICER SICER=$PATHTO PYTHONPATH=$SICER/lib export PYTHONPATH Tip: About duplicate reads One step of SICER is to remove duplicate read using remove_redundant_reads.py. “-t 1” is the default cutoff when doing duplicate reads removal. See line 60 of remove_redundant_reads.py . Solved: Error Report.   File "/depot/bioinfo/Projects/Kal/bean_GHvsTC/software/SICER_V1.1/SICER/src/remove_redundant_reads.py", line 84     print chrom, "\tPlus reads:",p_total, "\tRetained plus reads:", p_retained,     ";\tMinus reads:", m_total, "\tRetained...