Differences

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--- mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 11:07] – [Permissions] mkatari
+++ mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 11:50] (current) – [Controlling Jobs] mkatari
@@ Line 254: / Line 254: @@
 <code>
+[mkatari@hpc ~]$ history | grep bottom
   tail allusers.txt > bottomusers.txt
   ls -al bottomusers.txt
@@ Line 272: / Line 273: @@
 -r--r-----. 1 mkatari mkatari 772 Jun 11 14:01 bottomusers.txt
 </code>
+====== Transferring Files ======
+There are several ways to transfer files to a server. The most reliable and consistent way is to use ''scp''. scp is a combination of the cp copy command and ssh command for connecting securely. An important thing to note is that you can only use scp if the remote server accepts ssh connections. 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.
+One major advantage of using mobaxterm on windows machines is that it comes with some basic linux commands, including scp. On a mac, scp comes with the operating system. So if you want to copy a file that is on your Desktop to hpc from your laptop you can use the following command:
+<code>
+[2015-06-11 07:22.19]  ~
+[Manpreet.WIN-OAOVO3NM02E] ➤ cp allusers.txt Desktop/allusers_local.txt
+                                                                           ✔
+────────────────────────────────────────────────────────────────────────────
+[2015-06-11 07:22.37]  ~
+[Manpreet.WIN-OAOVO3NM02E] ➤ scp Desktop/allusers_local.txt mkatari@hpc.ilri.cgiar.org:
+Unauthorized access is prohibited.
+allusers_local.txt                        100%   18KB  18.2KB/s   00:00
+</code>
+the : at the end is very important because it tells the shell that is a server and not a file name. The : by itself puts the file in your home directory, but you can specify a specific path if you wanted to.
+Now to copy the file back to my computer I will use the following command. Note that this time I am also renaming the file on my computer.
+<code>
+[Manpreet.WIN-OAOVO3NM02E] ➤ scp mkatari@hpc.ilri.cgiar.org:allusers_local.txt ./return_allusers.txt
+Unauthorized access is prohibited.
+allusers_local.txt                        100%   18KB  18.2KB/s   00:00
+</code>
+====== Controlling Jobs ======
+The following commands and keyboard short-cuts can come in handing when you need to cancel, suspend, or start a job.
+^Command^Action^
+|ctrl-C|Terminate current running job|
+|ctrl-Z|Suspend Jobs|
+| bg | Once a job has been suspended ''bg'' can be put in the background |
+| fg | In order to put a background job in the foreground type ''fg''|
+| & | When executing a command and you want to put it in the background immediately put the ''&'' symbol at the end of the command.|
+| jobs | This gives a list of jobs (suspended, running, and terminating)|
+| top | This starts an interface where you can see all jobs. To see all jobs under your account type ''u'' and then when prompted, your account id.
+====== Commands for manipulating and querying files ======
+Some more cool commands
+^Command^Action^
+|less/more | read through the file without loading the entire file. Press spacebar to continue or q to quit. |
+|touch | create an empty file |
+|head | show the first few lines of the file|
+|tail | show the last few lines of the file|
+|cat | read through the file(s)|
+|grep | search for patterns in a file or files|
+|cut | separate file based on columns|
+|comm/diff | compare and see the difference between the files. The files have to be sorted before using either of these commands.|
+|split | splits file into smaller files based on the options|
+|sort | sort the file base on the options selected.|
+|wc | wordcount|
 ====== Exercise ======