mkatari-bioinformatics-august-2013-introlinuxnotes
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mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 09:22] – [Permissions] mkatari | mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 11:07] – [Permissions] mkatari | ||
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* 7 = read, write and execute | * 7 = read, write and execute | ||
+ | < | ||
+ | [mkatari@hpc ~]$ tail allusers.txt > bottomusers.txt | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -rw-rw-r--. 1 mkatari mkatari 772 Jun 11 13:54 bottomusers.txt | ||
- | wget ftp://ftp.jgi-psf.org/ | + | [mkatari@hpc ~]$ chmod u=+r-wx, |
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -r--r-----. 1 mkatari mkatari 772 Jun 11 13:54 bottomusers.txt | ||
- | [[ftp://ftp.jgi-psf.org/ | + | [mkatari@hpc ~]$ rm bottomusers.txt |
- | ]] | + | rm: remove write-protected regular file `bottomusers.txt'? y |
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | ls: cannot access bottomusers.txt: | ||
+ | </ | ||
+ | Notice that since we have taken away our own write permission to the file we can not automatically delete it. The shell is asking to change the permission so it can delete. If we have write permissions that it would have delete right away. | ||
+ | ====== History ====== | ||
+ | |||
+ | Your shell saves all your commands and you can access them using the up and down keys. | ||
+ | |||
+ | Typing the command “history” returns all the commands you have entered and a number assigned to it. | ||
+ | |||
+ | You can run a specific one again by typing ! (also called “bang”) Followed by the job number. | ||
+ | |||
+ | !! Will perform the most recent command. | ||
+ | |||
+ | In the example code below, '' | ||
+ | |||
+ | < | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | [mkatari@hpc ~]$ !1000 | ||
+ | tail allusers.txt > bottomusers.txt | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -rw-rw-r--. 1 mkatari mkatari 772 Jun 11 14:01 bottomusers.txt | ||
+ | [mkatari@hpc ~]$ !1002 | ||
+ | chmod u=+r-wx, | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -r--r-----. 1 mkatari mkatari 772 Jun 11 14:01 bottomusers.txt | ||
+ | </ | ||
+ | |||
+ | ====== Exercise ====== | ||
+ | |||
+ | - Download the file to your computer from the following url [[ftp:// | ||
+ | - Transfer it to your LinuxJune2015 directory on HPC. | ||
+ | - Gunzip the file and rename it to : Cassavagenes.txt | ||
+ | - Determine the number of different genes are present in the file. Hint – check the third column | ||
+ | - Save the rows that contain the word “gene” in the third column as a separate file. Call it “GeneTypes.txt” | ||
+ | - Create a directory called “Share” | ||
+ | - Move GeneTypes.txt into Share and change permissions on Share so others can read the file. | ||
====== Some useful information about linux ====== | ====== Some useful information about linux ====== | ||
mkatari-bioinformatics-august-2013-introlinuxnotes.txt · Last modified: 2015/06/11 11:50 by mkatari