There is a script available called get-obitools.py that will download and install the OBITools for you. pkg package, and follow the instructions of the installer. We specifically need Python 2.7, which can be downloaded from the python website. However, according to the documentation Mac users specifically need to “install a complete distribution of Python”, because “Python included in the system is not suitable for running the OBITools”. A version of Python should already be available on your system. Python is a programming language (just like html, CSS, C++, etc.). It is unclear if Clang also works for installing OBITools. GCC is not by default installed on your Mac, however you do have Clang, which is another compiler pretending to be gcc. Compiling is the process of taking source code (written in a programming language like Python or C++) and converting it into object code or machine code that your computer is actually able to understand and execute. Check prerequisitesīefore the installation, we need the following software to be installed already. If you don’t know how to get here: Applications > Utilities > Terminal. The full documentation of OBITools, which also includes information on the installation procedure. I first tried to install OBIT tools using their documentation. My computer ran for a couple of minutes, I agreed to install, upgrade or downgrade some packages, and it was done!Ĭonda install ecopcr Following documentation instructions failed… I stayed in the folder where I installed Miniconda (not sure if you need to, but it seemed right) and simply used: I tested the installation using conda list in the terminal, and it appeared to be successfully installed! Install OBITools I used my home directory and just accepted all default settings. sh file, and store it in the folder where you want to install Miniconda. If you don’t have Conda yet, you need to install it first. It can help you install a suite of bioinformatics software, among which OBITools. Someone pointed me to Bioconda: a package manager for bioinformatics software. I had two failed attempts (following the documentation, and through pip install), and one successful attempt (using Bioconda). In that case, Google is your best friend! It will probably redirect you to a blog or stackoverflow. It is possible that you might run into issues I don’t describe here. Not familiar with the terminal yet? Give this page a quick read. OBITools have to be installed using the terminal. This and all following blogs will be the result of my search to get a nicely working bioinformatics set-up on my own computer (MacBook Air MacOS High Sierra 10.13.6) and perhaps on a computing cluster. I have worked with Python before (OBITools is written in Python), but I am not yet very skilled working with the UNIX command line. Therefore, keeping in mind the future metabarcoding pipeline I will have to build, I am going to install the OBITools set (of which ecoPrimers is a part). OBITools seems to have very nice documentation and is used widely, which is quite useful in case I have questions or get stuck. Also, by writing and owning your own scripts you get a really good sense of what you’re doing, and you can easily replicate your work (in other words, you can just re-run your script instead of changing all the settings in an interface). However, I know that lot of bioinformatics folk are very happy using the UNIX command line interface for their work. The Primer3 website, or the implementation by NCBI called Primer-BLAST, seems very accessible if you’re used to using software with a graphical interface. The two options that seem to be widely used are the Primer3 website or the OBITools tool called ecoPrimers (see ‘ software for eDNA‘ for more information). So, the very first step in my metabarcoding research (after literature research of course!) was to design a species-specific primer.
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