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 sickle.
Programs used in this workshop¶
The following programs are used in this workshop:
All programs are already installed, all you have to do is load the virtual environment for this workshop. Once you are logged in to the server run:
You deactivate the virtual environment with:
NOTE: This is a python virtual environment. The binary folder of the virtual environment has symbolic links to all programs used in this workshop so you should be able to run those without problems.
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.
bowtie2 bowtie2-build velveth velvetg shuffleSequences_fastq.pl parallel samtools Ray
We will now iterate over all the programs in calling which on each of them. First make a variable containing all programs separated by whitespace:
$ req_progs="bowtie2 bowtie2-build velveth velvetg parallel samtools shuffleSequences_fastq.pl Ray" $ echo $req_progs bowtie2 bowtie2-build velveth velvetg parallel samtools shuffleSequences_fastq.pl
Now iterate over the variable req_progs and call which:
$ for p in $req_progs; do which $p || echo $p not in PATH; done /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/bowtie2 /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/bowtie2-build /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/velveth /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/velvetg /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/parallel /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/samtools /proj/g2014113/metagenomics/virt-env/mg-workshop/bin/shuffleSequences_fastq.pl
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. Installation procedures of research software often follow the same pattern. 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