Why perl for Science should die!

I think its fair to say the most popular programming/scripting language for Bioinformatics is Perl. My language of choice Python would certainly be coming in second. I reallly really don’t like perl, and I think it is a poor language for Science in general, here’s why!

1. Its hard to read

This is the biggest issue for me. Well commented Perl is actually pretty fun to read, its a punchy language so you don’t have to do too much scrolling to work out what is going on. However, the key point of that last comment is the word “comment”, poorly commented Perl scripts are a nightmare to read. And frankly, most of the scripts that I have read fall into this latter category. Turnover of people in Science is pretty high, so the idea using a language that makes it really hard for other people to just pick up where the other person left of is such a silly idea. The other key thing is that Science should be about transparency, and Perls silly syntax just adds another layer dust that hides mistakes and errors in logic. This is latter point is especially important when bioinformaticians are working with biologists who don’t know a computer language, essentially no oversight or review because the language is so god dam hard to understand unless you know the syntax.

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Making MrBays run on a mulitcore machine

So what makes the excellent phylogenetic program MrBays even better, multicore support!

MrBays itself is pretty easy to install on a linux machine just by following the configure file notes, however I found it a little more tricky to get it to run in multicore mode. Others might find this useful, so I through I would add it to my blog

First download and extract a copy of MrBays and naviage to the /src directory in the terminal.

Install the required libraries
>sudo apt-get install mpich2 libmpich2-dev libmpich2-1.2 libreadline6-dev

Run the following to configure.
>autoconf
>./configure --enable-mpi=yes --with-beagle=no
>make

As beagle is for graphics processors we want to turn that off for a normal PC like system.

Now in your home directory make a file called “.mpd.conf” add this line to the file but change the ‘secretword’ to what ever you like: “MPD_SECRETWORD=<secretword>”

Change the permissions so that only you can read and write
>chmod 700 .mpd.conf

Run the mpd in the background, it shouldn’t complain, but if it does do what it asks.
>mpd &

Now run the program on 6 cores (or how many you have available), stdout will be written to GT.txt, all this will run in the background due to “&”
>mpirun -np 6 mb trimmed_nex.txt > GT.txt &

You can check the progress by opening the output file or just typing:
>tail -f HGT.txt

Done!

Sources
http://matthewvavrek.com/2011/03/19/mrbayes-and-multicore-processors/
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_compile_single-_and_multi-processor_versions_on_SGI_machines.3F