The first UNIX commands I learned were ssh, scp and wget. ssh is used to connect to a server, while scp and wget are used for downloading and copying files.
ssh
Connecting and Disconnecting to the Server
To connect to a server, type: ssh user@server
where user is your username and server is the name of the server
You will be prompted to enter a password. The cursor does not move/show what you are typing as you enter the password.
To disconnect from the server, you can type exit or hit ctrl-D.
Networking
An IP address is made up of 4 bytes (32 bits). For example: 127.0.0.1 These addresses can also be associated with names like teamerlich.org.
When you use ssh, the server can be specified either by a name or an IP address.
Private/Public Key
Private/Public keys can be used for ssh passwordless login.
ssh-keygen generates two files: id-rsa (private) and id-rsa.pub (public). The private key is kept on the computer while the public key can be shared with others for secure login without a password.
scp and wget
Copy a local file to server
Download the chr 22 vcf file locally.
To copy the file to the server (run from downloads folder):
scp ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz maya@maya.teamerlich.org:~
Download a file directly to server
ssh to server:
ssh maya@maya.teamerlich.org
download file:
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
Download file from server to local computer
To copy from the server (run from where you want the file saved to):
scp maya@maya.teamerlich.org:~/ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz chr21.vcf.gz
File is saved in downloads folder with filename chr21.vcf.gz
Copy a directory to server
Created a new directory on mac called test1. test1 contains hello.txt and world.txt.
Copy to server:
scp -r test1 maya@maya.teamerlich.org:~
The -r option copies directories along with everything in them.
Use wget to download continuously
The -c option can be used to continue downloading a large file after the connection/download has been interrupted (as opposed to starting the download again).