As many microbiologists and other researchers working with high throughput sequencing I've decided to install and work with QIIME (a pipeline of different python scripts that makes our life a little easier).
I have to say beforehand I AM NOT A BIOINFORMATICIAN and I can be very clumsy with this kind of tools.
But I've learned that in microbiology we all have to learns or at least understand basic bioinformatics and programing notions if we want to have some edge and competitive performance.
So I jumped in the adventure of installing MacQiime
First I have to say that the installation in the Mac enviroment is less traumatic than my previuous experience in Ubuntu, I was running a virtual machine and when tried to update QIIME I got frustrating results with the VM and QIIME.
I recomend the Werner lab instructions for MacQIIME installation they are very well writen and fairly easy to follow.
One of the most commons errors in the installation of macqiime seems to be during the installation of BLAST, a tool for taxonomy assignment during the OTU's picking, it seems that a lot of people, like me, fail in the PATH modification step where you basically add the BLAST package to your PATH environment.
So what the heck is the PATH? first let me remind you again that I am not a bioinformatician but a poor computer owner/operator that runs a lot for help to the IT people.
The PATH is basically an "environment" that contains all the variables that are called by the system when programs are run, it connects and allows to call your software files, data and more. For the technological virgin as me the PATH is a long string of "no Idea what the f is this" characters and names that looks like this
-bash: /Users/juangiarrizzo:/Users/juangiarrizzo/blast-2.2.26/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin: No such file or directory
Lets go back to adding Blast to your PATH, in the instructions yo will see that to do so (after placing the BLAST package in your home) you have to modified a file called .profile.
THINGS THAT THEY DONT TELL YOU AND YOU PROBABLY NEED TO KNOW
1) .profile is a file that ir read every time you run your shell (the window where you type your commands)
2) Every time you write something in .profile you are saying to the system to ignore and overwrite what you wrote before
3) And more important you have to restart your shell to make the PATH modifications to work!!! this for the experts is a dah but from us mortals is not!! this measn you have to close and restart the terminal window so the modifications take place
4) Separate any new addings in the PATH with ":" otherwise you are just erasing the previous PATH statement.
Once you do a correct PATH addition for the BLAST package you should be able to locate the executable file "blastall" by typing: $ which blastal
If is not working this may be the causes:
1) You didn't restart the shell after modifying the PATH and adding the BLAST package (see instructions)
2) You overwrote the PATH by obsessively repeating the nano edit step (as I did)
3) Maybe you have the wrong name for the BLAST package in your $PATH, please note if you download the latest package the name is blast-2.2.26 and no blast-2.2.22 as it says in the instructions. Is OK to be a good instructions follower but reading is always advised.
I hope you find this helpful. You can also ask to to the QIIME forum if you run into other more complicated issue, you will find out that there are a lot of helpful and patience people waiting for you.
Cheers!!!
