Answer by slm for Can I zip an entire folder using gzip?

The gzip command will not recursively compress a directory into a single zip file, when using the -r switch. Rather it will walk that directory structure and zip each file that it finds into a separate file.

Example

before

$ tree dir1/
dir1/
|-- dir11
|   |-- file11
|   |-- file12
|   `-- file13
|-- file1
|-- file2
`-- file3

now run the gzip command

$ gzip -r dir1

after

$ tree dir1/
dir1/
|-- dir11
|   |-- file11.gz
|   |-- file12.gz
|   `-- file13.gz
|-- file1.gz
|-- file2.gz
`-- file3.gz

If you'd prefer to zip up the directory structure then you'll likely want to use the tar command, and then compress the resulting .tar file.

$ tar zcvf dir1.tar.gz dir1/

Example

$ tar zcvf dir1.tar.gz dir1/
dir1/
dir1/file1
dir1/file2
dir1/dir11/
dir1/dir11/file11.gz
dir1/dir11/file12.gz
dir1/dir11/file13.gz
dir1/file3

Which results in the following single file:

$ ls -l | grep tar
-rw-rw-r-- 1 saml saml  271 Oct  1 08:07 dir1.tar.gz

You can confirm its contents:

$ tar ztvf dir1.tar.gz 
drwxrwxr-x saml/saml         0 2013-10-01 08:05 dir1/
-rw-rw-r-- saml/saml         0 2013-10-01 07:45 dir1/file1
-rw-rw-r-- saml/saml         0 2013-10-01 07:45 dir1/file2
drwxrwxr-x saml/saml         0 2013-10-01 08:04 dir1/dir11/
-rw-rw-r-- saml/saml        27 2013-10-01 07:45 dir1/dir11/file11.gz
-rw-rw-r-- saml/saml        27 2013-10-01 07:45 dir1/dir11/file12.gz
-rw-rw-r-- saml/saml        27 2013-10-01 07:45 dir1/dir11/file13.gz
-rw-rw-r-- saml/saml         0 2013-10-01 07:45 dir1/file3