--- title: 'RNA-Seq Workshop 2019' disqus: hackmd --- RNA-Seq Workshop 2019 - Unix === ## Table of Contents [TOC] ## HTC Login Open a Mac terminal and ssh using the below command. Before proceeding make sure you have sremote access. ``` ssh <pittusername>@htc.crc.pitt.edu ``` Replace pittusername with your pitt id. Below is an example on how to login into HTC. ```bash $ ssh abc46@htc.crc.pitt.edu Warning: the ECDSA host key for 'htc.crc.pitt.edu' differs from the key for the IP address '136.142.217.118' Offending key for IP in /Users/Anish/.ssh/known_hosts:9 Matching host key in /Users/Anish/.ssh/known_hosts:12 Are you sure you want to continue connecting (yes/no)? yes abc46@htc.crc.pitt.edu password: Last login: Fri Sep 27 14:49:16 2019 from sremote-10-195-22-70.vpn.pitt.edu abc46: ~ $ ``` If you have successfully logged in, you should be able to see your login screen. ## Basic Commands I Few basic commands in unix are given below. Please note that, every command is followed by hitting enter. 1. You can view your login id, using the following command. ``` $ whoami abc46 ``` 2. To know your present working directory, simply type *pwd*. ``` $ pwd /ihome/uchandran/abc46/rnaseq_wkshop ``` 3. To list the contents of a directory, use the command *ls*. ``` $ ls tmp file.txt ``` We can also list them in a long list format. ``` $ ls -l drwxr-xr-x 3 abc46 uchandran 47 Oct 2 10:21 tmp -rw-r--r-- 1 abc46 uchandran 13 Oct 2 10:21 file.txt ``` 4. To create directories, we can use the command *mkdir*. ``` $ mkdir Jobs $ ls file.txt Jobs tmp $ ls -l total 30 -rw-r--r-- 1 abc46 uchandran 13 Oct 2 10:21 file.txt drwxr-xr-x 2 abc46 uchandran 0 Oct 2 10:28 Jobs drwxr-xr-x 2 abc46 uchandran 0 Oct 2 10:18 tmp $ pwd /ihome/uchandran/abc46/rnaseq_wkshop ``` 5. As you can see from the above *pwd* command, we have not changed directories by creating directories. To change directory, we use the command *cd*. ``` $ cd tmp/ $ pwd /ihome/uchandran/abc46/rnaseq_wkshop/tmp ``` :::info You can hit <tab> to auto-complete your commands and file/folder names. ::: 6. To clear the screen, just type the command clear and hit enter. ``` $ clear ``` 7. To get the history of commands used, just type history and hit enter. ``` $ history 1018 cd rnaseq_wkshop/ 1019 ls -lh 1020 ls 1021 mv file.txt ../ 1022 ls 1023 clear 1024 ls 1025 ls -lh 1026 pwd 1027 mkdir Jobs 1028 ls 1029 ls -lh 1030 mv ../file.txt . 1031 ls 1032 ls -lh 1033 ls -l 1034 cd tmp/ 1035 pwd 1036 history ``` :::info You can get documentation of each command in unix, by typing *man <command-name>*. For e.g., to get a manual page of the command *ls*, just type *man ls* and hit enter. ::: ## Basic commands II 1. We can copy files in unix using the command *cp*. ``` $ pwd /ihome/uchandran/abc46/rnaseq_wkshop $ ls file.txt Jobs tmp $ cp file.txt tmp/ $ ls file.txt Jobs tmp ``` To check if the file has been copied into the folder tmp, we can either: ``` $ cd tmp/ $ ls file.txt ``` or simply type ``` $ ls tmp/ file.txt ``` But to copy directories, we need use the option *-r*, which means copy contents recursively. Let's say we are trying the copy the tmp folder and its contents in Jobs folder. You would use the following command: ``` $ cp -r tmp Jobs $ ls Jobs tmp $ ls Jobs/tmp/ file.txt ``` 2. We can check the beginning and end of the files using *head* and *tail* commands. ``` $ head file.txt one two three four five six seven eight nine ten $ tail file.txt three four five six seven eight nine ten eleven twelve ``` 3. We can also search for a pattern/string using *grep* command. ``` $ grep "six" file.txt six ``` 4. You can also concatenate files using cat command. ``` $ cp file.txt file2.txt $ cat file.txt file2.txt > combined_files.txt $ ls $ combined_files.txt file2.txt file.txt ``` 5. wc gives the number of words, bytes and newline counts. ``` $ wc file.txt 12 12 63 file.txt $ wc combined_files.txt 24 24 126 combined_files.txt ``` ###### tags: `workshop` `RNA-Seq`