![]() ![]() They noted that getting up and running with R was not as seamless as one would like it to be and, to be honest, I have to agree, especially after typing the rest of this post out. I was in a conversation with an academic colleague (wicked smart dude) and the subject of installing R came up (NOTE: this will happen to you, too, if you ever have the misfortune to have a face-to-face convo with me -). Some excellent additional advice and “gotchas” by some super-helpful readers. return_allusers.txtĪllusers_local.txt 100% 18KB 18.NOTE: The comments are a must read for this. Note that this time I am also renaming the file on my computer. Now to copy the file back to my computer I will use the following command. The : by itself puts the file in your home directory, but you can specify a specific path if you wanted to. The : at the end is very important because it tells the shell that is a server and not a file name. ➤ scp Desktop/allusers_local.txt access is prohibited.Īllusers_local.txt 100% 18KB 18.2KB/s 00:00 ➤ cp allusers.txt Desktop/allusers_local.txt So if you want to copy a file that is on your Desktop to hpc from your laptop you can use the following command: On a mac, scp comes with the operating system. ![]() One major advantage of using mobaxterm on windows machines is that it comes with some basic linux commands, including scp. For example, if you are using a windows machine and have not setup a service to accept ssh connections, you can copy to your windows machines, but you can copy from your windows machine. An important thing to note is that you can only use scp if the remote server accepts ssh connections. scp is a combination of the cp copy command and ssh command for connecting securely. The most reliable and consistent way is to use scp. There are several ways to transfer files to a server. ![]() 1 mkatari mkatari 772 Jun 11 14:01 bottomusers.txt Transferring Files Tail allusers.txt > ~]$ ls -al bottomusers.txt The > sign redirects the output to a new file called ~]$ history | grep bottomġ002 chmod u=+r-wx,g=+r-wx,o=-rwx bottomusers.txt In the example code below, tail is used to get the last lines of the file allusers.txt. You can run a specific one again by typing ! (also called “bang”) Followed by the job number. Typing the command “history” returns all the commands you have entered and a number assigned to it. Your shell saves all your commands and you can access them using the up and down keys. 1 mkatari mkatari 381856 _2.fastq Directing standard output In the ls -l example, ls is the command and everything else are options that are ~]$ date Many commands/programs have options that are provided immediately following the command. In the example below, date is a command that is being executed with no arguments. If there is an output to the program it usually prints it on the screen (often referred to as the standard output) When your prompt returns, you know that the program has finished. Once you press enter the program will be executed. You should have a window popup on your computer that looks something like this.ĭelete everything to the right of the character Manpreets-MacBook-Pro:~ manpreetkatari$ ssh -X access is password: Last login: Wed Jun 3 15:49:01 on ttys000 This opens a tunnel to your computer allowing all windows to open in your computer.įor this to work you need X11 installed on your computer (MobaXterm already has one) In cases where a program requires a GUI, you should log in using the –X option. There are several different shells, but the one used often is called “bash”, which is a mixture of a bunch of other shells. It is simply a prompt the awaits your command. However for linux it is a command-line interpreter called shell. The standard user interface for personal computers is a GUI (Graphical User Interface).
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