The final step in making useful pipelines is handling files and directories, since any given 3rd party bioinformatics program will undoubtedly produce output and log files, while needing an organized collection of input files.
The following examples will use real-world examples and programs. To see the installed programs in my (Nishimura) infrastructure, do:
$ ls /firstname.lastname@example.org/bin
You will see a long list of programs and directories which contain programs. To activate this environment, you must source the configuration script:
$ source /email@example.com/paths.bashrc
Now you can access these programs on the command line. For example, try: