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--- mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:40] – mkatari
+++ mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 09:11] – [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>
+        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 ===