Checking required software¶
An often occuring theme in bioinformatics is installing software. Here we wil go over some steps to help you check whether you actually have the right software installed. There’s an optional excerise on how to install the quality trimmer sickle.
Programs used in this workshop¶
The following programs are used in this workshop:
Using which to locate a program¶
An easy way to determine whether you have have a certain program installed is by typing:
where programname is the name of the program you want to use. The program which searches all directories in $PATH for the executable file programname and returns the path of the first found hit. This is exactly what happens when you would just type programname on the command line, but then programname is also executed. To see what your $PATH looks like, simply echo it:
For more information on the $PATH variable see this link: http://www.linfo.org/path_env_var.html.
Check all programs in one go with which¶
To check whether you have all programs installed in one go, you can use which. In order to do so we will iterate over all the programs and call which on each of them. First make a variable containing all programs separated by whitespace:
req_progs="bowtie2 bowtie2-build velveth velvetg parallel samtools interleave-reads.py diamond MEGAN fastqc sortmerna prokka MinPath1.2.py bedtools" echo $req_progs
Now iterate over the variable req_progs and call which:
for p in $req_progs; do which $p || echo $p not in PATH; done
In Unix-like systems a program that sucessfully completes it tasks should return a zero exit status. For the program which that is the case if the program is found. The || character does not mean pipe the output onward as you are probably familiar with (otherwise see http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-4.html), but checks whether the program before it exists succesfully and executes the part behind it if not.
If any of the installed programs is missing, try to install them yourself or ask. If you are having troubles following these examples, try to find some bash tutorials online next time you have some time to kill. Educating yourself on how to use the command line effectively increases your productivity immensely.
Some bash resources:
- Excellent bash tutorial http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html
- Blog post on pipes for NGS http://www.vincebuffalo.com/2013/08/08/the-mighty-named-pipe.html
- Using bash and GNU parallel for NGS http://bit.ly/gwbash
(Optional excercise) Install sickle by yourself¶
Follow these steps only if you want to install sickle by yourself.
From the sickle project description: “Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3’-end of reads and also determines when the quality is sufficiently high enough to trim the 5’-end of reads. It will also discard reads based upon the length threshold.”
Installation procedures of research software often follow the same pattern, so it’s useful to learn how to do this. Download the code, compile it and copy the binary to a location in your $PATH. The code for sickle is on https://github.com/najoshi/sickle. I prefer compiling my programs in ~/src and then copying the resulting program to my ~/bin directory, which is in my $PATH. This should get you a long way:
mkdir -p ~/src # Go to the source directory and clone the sickle repository cd ~/src git clone https://github.com/najoshi/sickle cd sickle # Compile the program make # Create a bin directory mkdir -p ~/bin cp sickle ~/bin