Trouble installing cd-hit

Question

[nlehmann]

Hi,

I'm trying to install cd-hit on a Mac osX el Capitan, but I can't find what's going wrong neither in the forum neither in the readme file. Any help would be welcome. make seems to go fine, and make openmp=no too. But then I cannot use any cd-hit command. Thanks !

This is what I get :

$ make
g++  -DNO_OPENMP -O2  cdhit-common.c++ -c
g++  -DNO_OPENMP -O2  cdhit-utility.c++ -c
g++  -DNO_OPENMP -O2  cdhit.c++ -c
g++  -DNO_OPENMP -O2  cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
g++  -DNO_OPENMP -O2  cdhit-est.c++ -c
g++  -DNO_OPENMP -O2  cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
g++  -DNO_OPENMP -O2  cdhit-2d.c++ -c
g++  -DNO_OPENMP -O2  cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
g++  -DNO_OPENMP -O2  cdhit-est-2d.c++ -c
g++  -DNO_OPENMP -O2  cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
g++  -DNO_OPENMP -O2  cdhit-div.c++ -c
g++  -DNO_OPENMP -O2  cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
g++  -DNO_OPENMP -O2  cdhit-454.c++ -c
g++  -DNO_OPENMP -O2  cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454


$ make openmp=no
make: Nothing to be done for `all'.

$ cd-hit -i all.fasta -o clusters -c 0.4 -n 2 -M 6000 -T 6
-bash: cd-hit: command not found

[Pierre Lindenbaum]

nothing is wrong with make. You just have to append the directory to your PATH ... http://www.linfo.org/path_env_var.html

[Md]

How to do CD-HIT clustering for phylogeny analysis, my doubt is how it is working, if we see manual, it will show cd-hit -i input_reads.fasta -o output, but we will be having one fasta file from one organisms, so how it will cluster taking one fasta file, if input file is single fasta file, or do we have to merge all file into single file, if it si how to do it. or if we keep all fasta file in single directory, than what will be the command.

Answer 1

[Neilfws]

The compiled executables are not in your PATH. So you have multiple options:

(1) add the directory where they reside to your PATH;

(2) move them to a directory which is in your PATH;

(3) run them from the directory where they are using e.g. ./cd-hit or by specifying the full path to the executable e.g. /path/to/cd-hit.

Since you're using OSX, consider Homebrew. It includes many science packages including CD-HIT and will place the executables in /usr/local/bin:

brew install cd-hit

[nlehmann]

Thanks a lot ! It works when I add it to my PATH.