Installing a new software the old fashioned way (and a glimpse of things to come)
Work from/to your Assignment_1/ folder. Create a file MyCommands.txt. Keep a record explaining what you did for this assignment in MyCommands.txt.
2 pts. 1. Download the file http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz. Put it in your Assignment_1/ folder. Decompress it. Use any method of your choosing.
### Muscle is a sequence alignment software. We will learn more about it later in the semester.
2 pts. 2. Dang! Look at that name! Rename muscle3.8.31i_86linux64 to a much simpler, more palatable name like muscle.
2 pts. 3. Modify your ~/.bash_profile so that muscle can be ran from anywhere without invoking absolute or relative paths.
2 pts. 4. Make a bash script called run_muscle.sh that:
i) Concatenates all 16S fasta files from the 16S/ folder into a single multifasta called 16S.fasta.
ii) Runs muscle on the 16S fasta file and generates an output file named 16S.aligned. ### NOTE: To learn how to do this, type “muscle” in the terminal to see a quick list of options.
iii) Tells you that the “Alignment is complete!” when the job is done.
iv) Make it executable.
v) Run it.
2 pts. 5. Create a regular expression that will get all (and only) the desired lines from Regex.input (see Regex.output for desired output).
i) Write that regular expression inside a file called MyRegex.txt.
ii) Test it with grep and write the output in output.txt
### Note: this is a gene ontology output file (P = biological_process, F = molecular_function, C = cellular_component).

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