9 Using nohup and other tips and tricks

Bash scripting using nohup

Fist step is to write your script into a text editor (vi or nano). I suggest using vi as it is a very powerful text editor with plenty of useful shortcuts. You can find more information on vi here.

  1. To create a new file the format of the command is as follow :
vi script.sh

First we call the program vi followed by the name of file to create. The extension of the file needs to reflect the type of file you want to create (i.e. for a python script the extension would be .py, a bash script would be .sh, and a simple text file would be .txt. Since the commands we are writing are for executed by bash we need to use the extension .sh.

  1. In the new opened window write your script. To start typing with vi press the i touch.

  2. Once you are done exit vi by pressing esc then : followed by w and q. If you want to exit without saving your changes press q and ! instead.

  3. Make your script executable. If you look at the file using ll the script should now be green and followed by *.

chmod +x script.sh
  1. Run using nohup
nohup ./script.sh &

After pressing nohup the prompt will print your process ID in the following format [1] xxxxxxxx and print the following : nohup: ignoring input and appending output to 'nohup.out' Press enter again to return to the prompt. Your process is completed when you get the following [1]+ Done nohup ./script.sh. If nohup exits there was an error running the script. To view the output and the find out the error, view the report using less nohup.out. Exit less with q

  1. View jobs status
jobs
  1. Once nohup is done running your script it will write Done

Other tips and tricks

To move or copy many files listed in a text files

xargs -a file_list.txt mv -t /path/to/directory

Moving files using SCP

To move file from your computer to the server, from your local terminal

scp filename.txt servername@server.bio.uqam.ca:/home/user/pathway/todirectory

To move file from your the server, to your computer

scp kvilleneuve@titan.bio.uqam.ca:/home/kvilleneuve/filename.txt .

Renaming files

Replace the pattern in brackets for the section of words you want to remove from the name of your file.

for i in *.fastq; do mv $i "$(echo $i | sed s/"_R1.fastq.interleave.fastq.trim.fastq.gz."/./)"; done

Rename multiple files using a text file (example:`rename.txt) consisting of the following 2 columns separated by a space :old_namenew_name` (No column name required)

while read old new ; do mv -v "$old" "$new" ; done < rename.txt

Extract scaffholds based on name and coordinates using samtools

Copy the scaffhold name followed by the coordinates in a vi file. Example : contig-115_1168:1-955

Extract the sequence identified in the vi file into a new file using samtools

for i in `cat scaff`; do samtools faidx 2000kb.fa $i >>16S_2Kb.fna; done