This week is a “half-module” as it overlaps with one of the two “instructional breaks” this semester. We will only meet on Thursday and the chapter to be read (Buffalo Chapter 6) is a very short one.
We will talk about downloading and transferring data in the shell, checking file integrity, and working with compressed data. We will also do a recap of loops and Bash scripting.
Some of the things you will learn this week:
How to download data using the shell tools wget (and curl).
How to transfer data (in particular to and from OSC) using rsync and sftp.
How to check file integrity using “checksums”, to ensure that you have downloaded/transferred files completely.
How to compress and uncompress data using gzip, and how to work with gzipped data.
Optional: Basics of process management – in particular, how to send processes to the background.
This chapter deals with commands for downloading data, remote copying, checking data integrity after download or transfer, and working with compressed data. Despite the title “Bioinformatics Data”, there is little in the chapter that applies only to bioinformatics data.
If you have additional time to spend on the course this week, I recommend you review the material we’ve covered so far, as we will switch gears next week and will be covering Python for much of the rest of the course.
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