This is Readme for first set of Linux excercises. =Task 1.2.1= Since we can not ssh to other server outside, we have to use what we have: your vagrant virtual machine; #change directory from your home to soft cd ~/data/ex1 #go to home dir cd cd data/ex1 #this will connect to your virtual machine as user vagrant ssh localhost #when asked for password, just type: vagrant #it prints: #Welcome to Ubuntu 12.04 LTS (GNU/Linux 3.2.0-23-generic x86_64) #now you are logged again as vagrant, but moved automaticaly to your home directory #Q1: how do you check it? #to finish being logged via ssh: exit # =Task 1.2.3= #Create few files using touch command: touch file1.txt touch file2_long_name.dat #list the directory content =Task 1.2.4== #check were you are right now in the diretory structure pwd #jumpt one directory above cd .. #explore what is at the / of the file system cd / ls #jump back to the directory you have been before cd - #or if you are lost: /home/vagrant/data/ex1 #there is a directory there called dir_tree #one of the subdirectories contains file secret_file Q: what is the secret? =Task 1.2.5= #go to /home/vagrant/data/ex1/dir_tree/work3 # jump to your /home/vagrant/data/ directory using 3 different ways (absolute, combination of ../, special sign ~) =Task 1.2.6= #go to /home/vagrant/data/ex1/perm_dir # list files with permissions (ls -l) in this directory Q1: change permissions for file6.txt. What is the first line? Q2: there are two script files ending with sh. To execute them try: ./my_script1.sh ./my_script2.sh What is the difference? Q3: make my_script2.sh executable by changing permissions +Task 1.2.7= Q1:copy file2.txt to file2.1.txt Q2: rename file2.1.txt to file2.1.NEW.txt Q3: copy file6.txt to student1 directory Q4: go to student1 directory. Link both *sh scripts so these appear as soft links in this directory =Task 1.2.8= cd /home/vagrant/data/ex1/file_content #displays content of the file screen by screen more myfile04.txt #same as above but you can scroll back less myfile04.txt #displays just the first 10 top lines of the file head myfile04.txt #displays the first 100 lines head -100 myfile04.txt #displays just the last 10 lines of the file tail myfile04.txt #displays the last 100 lines of the file tail -100 myfile04.txt wc myfile04.txt #newline, word, and byte counts for the file # just count the lines of the file wc -l myfile04.txt =task 1.2.9= Q1: gzip file1.gtf Q2: go to student2 directory, untar the tar filelocated there Q3: go to student3 directory (in ..), create gzipped tar from 3 files located there =task 1.2.10= cd /home/vagrant/data/ex1/checksums Q1: there are 3 gzipped files there. Which ones are identical?
=Task 1.2.11= #goto /home/vagrant/data/ex2/pattern #display the number of .txt files in this directory ls *.txt | wc -l #we create a new file listing all the names of m*.txt files, one name per line ls f*.txt > list_of_txt_files_starting_with_f.fof #checking what is inside more list_of_txt_files_starting_with_f.fof
cd ex34 ls # fix the fasta headers using provided python script # reformat the fasta using fastareformat # index the genome file for bwa # map the genomic chicken reads using bwa # repeat every mapping exercise for each of the mappers described on the main page # sort and index BAM results # view the results in IGV using your toy genome