Introducing the Shell


Figure 1

Folder organization diagram showing a parent directory called dc_workshop, with tree subdirectories called data, mags, and taxonomy. Insida data there is another one called untrimmed_fastq, and inside taxonomy there is another one called mags_taxonomy.

Navigating Files and Directories


Figure 1

File permission parameters The file permission parameters described in the text (-rw-rw-r--) showing which of the slots correspond to who has permissions, and a legend showing the meaning of the letters. Here the three positions that relate to the file owner are rw-. The r means that you have permission to read the file, the w indicates that you have permission to write to (i.e. make changes to) the file, and the third position is a -, indicating that you don’t have permission to carry out the ability encoded by that space (this is the space where x or executable ability is stored, we’ll talk more about this in a later lesson).


Figure 2

The file permission parameters described in the text (-rw-rw-r--) showing which of the slots correspond to who has permissions, and a legend showing the meaning of the letters.

Figure 3

Filesystem diagram with folders: Users/thing/backup/2012-12-02, Users/thing/backup/2012-01-08, Users/thing/backup/2013-01-27, Users/backup/original, Users/backup/pnas_final, and Users/backup/pnas_sub

Working with Files and Directories


Redirection


Writing Scripts and Working with Data


Figure 1

nano screen with the name of the file in the top bar, a blank screen to write in the middle, and a bottom bar with the shortcuts for the available nano instructions.

Figure 2

The same screen as before but now it has text in the middle part.

Figure 3

Download data with R Studio.

Figure 4

Download data with R studio.

Figure 5

Download data with R studio.

Figure 6

Download data with R studio.

Figure 7

Upload data with R studio.

Figure 8

Upload data with R studio.

Figure 9

Upload data with R studio.

Figure 10

Upload data with R studio.

Project Organization