TP 2.1: Files and directories

Goal: Move inside tree structure.

The purpose of this practice is to put you in situation: You have launched calculations (in work space) and must organize and store results inside your personal backup space (save). Fasta files will be stored into data directory from save space. Following the same logic, blast files will be stored into blast directory in save space.

Reminder

Current state of your directories:

/home/<username> : configuration files
/save/user/<username> : backup space, empty
/work/user/<username> : working space, files resulting from analysis

Prerequisite¶

Before starting this practice, please type the following command:

cp -r /home/formation/save/tp_unix/data/* ~/work

Create a project directory¶

Question

In you save space, create a folder called tp_unix, go in this folder.

Solution

cd /save/user/<username>
mkdir tp_unix
cd tp_unix

You must replace <username> by your username

Structure the projet¶

Question

Create the sub-directories data, blast_result.

Solution

mkdir data
mkdir blast_result

or in one line

mkdir data blast_result

Visualize the content of your working directory¶

Question

List all the files inside the work directory.

Solution

Many possibilities (not exaustive):

by going inside the directory
```
cd
cd work
ls
```
by using relative path
```
ls ../../work/user/<username>
```
by using the absolute path
```
ls /work/user/<username>
```
by passing by the home directory shortcut.
```
ls /home/<username>/work
```
the same, but using the shortcut ~ that go to the home directory.
```
ls ~/work
```

Organize data¶

Question

Move the files *.fasta inside directory tp_unix/data; check that none exists in work directory.
Copy blast result files (*.blast) inside directory tp_unix/blast_result.

Solution

For 1:

cd /home/<username>/work
mv *.fasta ~/save/tp_unix/data
ls

For 2:

cp *.blast ~/save/tp_unix/blast_result

Create symbolic link (shortcut)¶

Question

In order to avoid multiple copies of a file, a good practice is to use symbolic link (shortcut) pointing on this file.

Go in the directory ~/work and créate a symbolic link that points to the file ~/save/tp_unix/data/ab005233.fasta.

List in detailled manner the files inside your space work.

Solution

One solution

cd ~/work
ln -s ~/save/tp_unix/data/ab005233.fasta
ls -l

or an equivalent solution

ln -s ~/save/tp_unix/data/ab005233.fasta ~/work
cd ~/work
ls -l