Chapter12 Bio@R_322_4045@ics Shell Scripting, Writing Pipelines, and Parallelizing Tasks
We’ll see how to write rerunnable Bash shell scripts, automate fileprocessing tasks with find and xargs, run pipelines in parallel, and see a simple makefile.
Basic Bash Scripting
Writing and Running Robust Bash Scripts
1. A robust Bash header
#!/bin/bash
set -e
set -u
set -o pipefail
(1) This is called the shebang, and it indicates the path to the interpreter used to execute this script.
(2) 若某一行shell命令error，shell默认仍会执行完整个命令。set -e 使得error时直接终结整个命令，但某些可能不会有影响的error，如test -d file.txt will return a nonzero exit status if its argument is not a directory，却不会终结。
(3) 若某一命令含有未定义路径，shell仍会执行，如 rm -rf $TEMP_DIR/. If the shell variable $TEMP_DIR isn’t set, Bash will still substitute its value (which is nothing) in place of it. The end result is rm -rf /。使用set -u阻止类似命令的执行。
(4) 即使设置了set -e ，但在pipe中也只有最后一个program出现error时，才会导致程序跳出。set -o pipefail使得pipe 中任一program error都会终止程序。
2. Running Bash scripts
two ways:
bash script.sh: can run any script (as long as it has read permissions) with bash script.sh
./script.sh: might use interpreters other than /bin/bash (e.g., zsh, csh, etc.)
executable permissions:
$ chmod u+x script.sh
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