installing mothur

Commands in mothur
1

Hi everybody,
I am very sorry for coming with a basic question: how to install mothur?
I followed the instruction on the Wiki page, but it does not work actually…

  1. I downloaded the last version of mothur
  2. the folder is automatically unzipped and it is in Downloads folder
  3. I open the terminal and enter into the folder
  4. write “make” in the command line

—> -bash: make: command not found

I actually tried several other options, moving the folder somewhere elses but still I got the same problem…

DO you mind helping me please?! I am a bit lost and trying the learn right now…

thanks
anna

2

The error you are getting indicates you do not have make installed on your machine. Most of our users download the executable version. Here’s a link to our latest release, https://github.com/mothur/mothur/releases. Choose from the first 6 downloads options based on your OS. You simply download a zip file. Decompress it and start using mothur.

3

Hello,
I’m having a similar issue.
I downloaded the latest version (1.36.1) of mothur: Mothur.mac_64.OSX-10.9.zip
The folder was automatically unzipped.
I then CD into the mother folder, where the mothur executable file is.
when I try to enter into mothur through ./mothur I get the error “Illegal instruction: 4”
How do I fix this?
Thank you for any help you could provide

4

Hi,

Might have been better to create a new post.

Most likely that pre compiled binary supplied ( OSX 10.9 ) has been optimised for that version and not runable on older OSX version. Downloaded compiled OSX version does run on my 10.10.5

Download source code and compile yourself if that’s an option? Or ask if the developers can recompile a different version using -mmacosx-version-min

What version of OSX are you using?

Ian

5

Hi Ian,
I’m using OSX Lion 10.7.5. I was worried that may be the issue.
I’ll try downloading the source code.

Meaghan

6

The executable version of mothur we have available for Mac is compatible with OSX 10.9 or greater. There are a two options.

  1. Upgrade your version of OSX. Apple makes this super easy, :slight_smile: and the latest features are nice as well.
  2. Build mothur from source. You will need to install Xcode and Xcode tools to get the compilers you need to build. You will also need to install Boost if you want to use the new gz options. Once you have the compiler and boost installed, download mothur’s source here, https://github.com/mothur/mothur/releases. Open a terminal window, cd into the directory and type make. You should see something like:

sarahwestcott$ make
c++ -O3 -DBIT_VERSION -DRELEASE_DATE="“7/27/2015"” -DVERSION="“1.36.1"” -DUSE_READLINE -DUSE_BOOST -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -arch x86_64 -c -o source/averagelinkage.o source/averagelinkage.cpp
c++ -O3 -DBIT_VERSION -DRELEASE_DATE="“7/27/2015"” -DVERSION="“1.36.1"” -DUSE_READLINE -DUSE_BOOST -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -arch x86_64 -c -o source/calcsparcc.o source/calcsparcc.cpp
…

Once the build finishes you are ready to use mothur.