Hi,
I'm trying to use RAxML to do the phylogenetic analysis for my data. I'd like to compile it on my mac. By following the guidebook, I use command "makefile" to compile Makefile.AVX2.gcc, but RAxML seems not installed successfully because when I type "raxmlHPC", it returned "command not found". There're a lot of Makefile* in my folder:
Makefile.AVX2.gcc
Makefile.AVX2.HYBRID.gcc
Makefile.AVX2.mac
Makefile.AVX2.MPI.gcc
Makefile.AVX2.PTHREADS.gcc
Makefile.AVX2.PTHREADS.mac
And the same format for SSE3. I don't know which one to choose to do makefile.
I read the README instruction, there are three different version corresponding to different Makefile (Sequential version; Pthreads version and Coarse-grain MPI version),
My mac was bought in 2016 so it's pretty new, can anybody tell how to install RAXML here successfully?
Thank you very much.
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horsedog •
1 answer
If you compiled, no errors returned and you want to execute the program from inside the source folder, you have to type "./raxmlHPC" (no " when you type in the terminal)
Another way less headache is to use bioconda. Some simple steps in the followings:
- Install miniconda2 (or 3)
- Add bioconda channel
- Install raxml with conda: conda install raxml
- Run raxmlHPC
Worked on my mac High Sierra
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Have you installed a compiler? Does the make command execute without errors? Are RAxML binaries being created? If yes, then you just need to add them to your $PATH, i.e. you need to tell your shell about them. It doesn't just automagically know where everything is..