gzip and tar

Author: HadrienG

README.md

@@ -5,6 +5,7 @@ bioinformatics subjects:
 
 ### Table of contents
 
+* [Introduction to Unix](unix/first_steps.md)
 * [16s Metabarcoding Analysis](16s.md)
 * [Whole Metagenome Sequencing](wms.md)
 * [Metagenome Assembly](meta_assembly.md)

unix.md unix/first_steps.mdunix.md renamed to unix/first_steps.md

@@ -124,7 +124,9 @@ Change current working directory The cd command will change the current working
 
 `cd ngs_course_data [enter]`
 
- Now use the pwd command to check your location in the directory hierarchy.
+Now use the pwd command to check your location in the directory hierarchy.
+
+Change again the directory to `Module_Unix`  
 
 **ls**  
 List the contents of a directory To find out what are the contents of the current directory type **ls** [enter] The ls command lists the contents of your current directory, this includes files and directories You should see that there are several other directories.
@@ -296,12 +298,9 @@ The wildcard * symbol represents a string of any character and of any length.
 
 <p style="text-align: center;">
   <a href="http://77.235.253.122/tutorials/wp-content/uploads/2015/06/Unix_exercise12.png"><img class="alignnone size-full wp-image-443" src="http://77.235.253.122/tutorials/wp-content/uploads/2015/06/Unix_exercise12.png" alt="Unix_exercise12" width="865" height="267" /></a>
-</p> For more information on Unix command see EMBNet UNIX Quick Guide.  
+
+For more information on Unix command see EMBNet UNIX Quick Guide.  
 
 <h1 style="text-align: center;">
-  END OF THE MODULE
+  End of the module
 </h1>
-
-<p style="text-align: center;">
-  <a href="http://77.235.253.122/tutorials/all-courses/"Back to all courses</a>
-</p>

unix/fully_walking.md

@@ -0,0 +1,64 @@
+# Introduction to Unix (continued)
+
+In this part of the Unix tutorial, you will learn to download files, compress and decompress them, and combining commands
+
+## Download files
+
+`wget` can be used to download files from internet and store them. The following downloads and stores a file called to the current directory.
+
+`wget https://raw.githubusercontent.com/HadrienG/tutorials/master/LICENSE`
+
+will download the file that is located at the above URL on the internet, and put it **in the current directory**. This is the license under which this course is released. Open in and read it if you like!
+
+The `-O` option can be used to change the output file name.
+
+`wget -O GNU_FDL.txt https://raw.githubusercontent.com/HadrienG/tutorials/master/LICENSE`
+
+You can also use wget to download a file list using -i option and giving a text file containing file URLs. The following
+
+```
+cat > download-file-list.txt
+url_1
+url_2
+url_3
+url_4
+[CTRL-C] (to exit cat)
+```
+
+`wget -i download-file-list.txt`
+
+## Compressing and decompressing files
+
+### Compressing files with gzip
+
+gzip is a utility for compressing and decompressing individual files. To compress files, use:
+
+`gzip filename`
+
+The filename will be deleted and replaced by a compressed file called filename.gz To reverse the compression process, use:
+
+`gzip -d filename.gz`
+
+Try it on the License you just downloaded!
+
+### Tar archives
+
+Quite often, you don't want to compress just one file, but rather a bunch of them, or a directory.
+
+tar backs up entire directories and files as an archive. An archive is a file that contains other files plus information about them, such as their filename, owner, timestamps, and access permissions. tar does not perform any compression by default.
+
+To create a gzipped disk file tar archive, use
+
+`tar -czvf archivename filenames`
+
+where archivename will usually have a .tar .gz extension
+
+The c option means create, the v option means verbose (output filenames as they are archived), and option f means file.
+
+To list the contents of a gzipped tar archive, use
+
+`tar -tzvf archivename`
+
+To unpack files from a tar archive, use
+
+$ tar -xzvf archivename