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--- mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:40] – mkatari
+++ mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 09:19] – [File manipulation] mkatari
@@ Line 143: / Line 143: @@
 </code>
-SLIDE16
+===== Finding Your Way =====
+Often you will get lost on the hpc and you will need to know where you are, which computer did you log into, or even which account have you logged into. Below are some simple commands that help you find your way.
+<code>
+[mkatari@hpc ~]$ whoami
+mkatari
+[mkatari@hpc ~]$ pwd
+/home/mkatari
+[mkatari@hpc ~]$ hostname
+hpc.ilri.cgiar.org
+</code>
+===== File manipulation =====
+Useful commands for manipulating files and directories. To get details about how to use the commands type man <command>.
+^Command ^Action ^
+|mkdir | make a directory |
+|rmdir | remove a directory (only works if the directory is empty ) |
+|cd    | change directory |
+|pwd   | present working directory |
+|ls    | list of files and directories in the directory. You can use wild card to look for specific files. You can also use -l to see details such as permission for files and directories |
+|cp    | copy a file and/or directories. Use -r to recursively copy.  |
+|mv    | move a file. It will copy and then delete the source. This can be used to rename files as well. |
+|rm    | remove a file |
+<code>
+[mkatari@hpc ~]$ mkdir temp
+[mkatari@hpc ~]$ cd temp/
+[mkatari@hpc temp]$ ls
+[mkatari@hpc temp]$ cp ../allusers.txt ./
+[mkatari@hpc temp]$ ls
+allusers.txt
+[mkatari@hpc temp]$ mv allusers.txt allusers.backup
+[mkatari@hpc temp]$ ls
+allusers.backup
+[mkatari@hpc temp]$ rm allusers.backup
+[mkatari@hpc temp]$ ls
+[mkatari@hpc temp]$ cd ../
+[mkatari@hpc ~]$ rmdir temp/
+</code>
+====== Permissions ======
+There are three levels of permissions that can be assigned to all files, programs, and directories
+  * Read: open the file and copy it
+  * Write: edit the file and delete it
+  * Execute: Run the commands in the file or change into the directory if it is a directory
+There are also three different levels of users:
+  * User – you
+  * Group – A collection of users that are in a group
+  * Everyone - Not just the people who have accounts on the machine but if the directory is open to the public and any one.
+The commands used to change owner, group, and specific permissions are:
+  * chown – changes the owner
+  * chgrp – changes the group
+  * chmod – change read, write, and execute permissions
+    * +/- r = read
+    * +/- w = write
+    * +/- x = execute
+    * u = user level
+    * g = group level
+    * o = others
+    * a = all
+  * chmod can also use three numbers to set permissions where the value of the number represents a specific combination of rwx and their order assigns it to the different levels (u,g,o)
+        wget ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/v5.0assembly/cassavaV5_0.chromsomesRomanNumerals.fa.gz
+[[ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/annotation/Mesculenta_147_gene.gff3.gz
+]]
 ====== Some useful information about linux ======
 === Environment variables and PATH ===