I used to work with windows based Mothur. I decided to go with Linux-64 since I got half a million sequences.
I really have problems with installing the v.1.21.0 on Ubuntu 11.04, even I followed the instruction accordingly. When I type “./mothur”, terminal gives " ./mothur: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory ". The Ubuntu system is new and fully updated. Can I have an older version somewhere?
Another thing is that I do not know what is “source code” and “executables”? Do I need both of them or just one? Why there is not makefile in “executables”?
I was really puzzled in the very beginning.
Please help me.
You haven’t said which of the available methods you;re using to install mothur.
You may well find that Ubuntu by default provides libreadline.so.6 rather than libreadline.so.5. You’d be able to overcome that problem by building mothur from source code, which will use the later version of readline. Or you may have the option - I don’t use Ubuntu myself - of installing an earlier version of readline explicitly. On Debian the package would be libreadline5 .
- Donald Neal
The University of Waikato
Re-reading your original post i realise my previous answer may not have helped you a lot.
Software is generally written as a language which humans (well, some of them) can read and write. This is usually called “source code” because it is the source from which the stuff the computer actually runs is generated. The makefile is used in that process of generating the executable code the computer really runs.
Your choices are
i) Build mothur from source code. If you don’t know what source code is, that’s probably not your best option.
ii) Install executables supplied. I assume you have already done this. The catch is that these only work with specific versions of the software libraries which provide functions which mothur uses. That means you will need to install the package libreadline5.
- Donald Neal
The University of Waikato
I agree with Donald. But if you decide to build from source, here’s some tips:
- Set the following makefile options:
USEMPI ?= no
64BIT_VERSION ?= yes
USEREADLINE ?= yes
CYGWIN_BUILD ?= no
USECOMPRESSION ?= no
RELEASE_DATE = "“7/27/2011"”
VERSION = "“1.21.0"”
You will also need to modify the 64bit section because you are running Linux, so here’s what that part of the make file will look like:
ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are using centos uncomment the following lines
CXX = g++44
#if you are a mac user use the following line
#TARGET_ARCH += -arch x86_64
#if you using cygwin to build Windows the following line
#CXX = x86_64-w64-mingw32-g++
#CC = x86_64-w64-mingw32-g++
#TARGET_ARCH += -m64
#if you are a linux user use the following line
CXXFLAGS += -mtune=native -march=native -m64
CXXFLAGS += -DBIT_VERSION
After you have modified the makefile and saved it. Open terminal and cd into the folder were the source is. Then all you need to do is type make. You will see output like:
g++44 -O3 -DBIT_VERSION -DRELEASE_DATE="“7/27/2011"” -DVERSION="“1.21.0"” -DUSE_READLINE -I. -mtune=native -march=native -m64 -c -o ace.o ace.cpp
g++44 -O3 -DBIT_VERSION -DRELEASE_DATE="“7/27/2011"” -DVERSION="“1.21.0"” -DUSE_READLINE -I. -mtune=native -march=native -m64 -c -o addtargets2.o addtargets2.cpp
venncommand.o viterbifast.o weighted.o weightedlinkage.o whittaker.o writechhit.o fisher2.o metastats2.o -lreadline -lncurses
I hope this helps,
Hi, thanks very much for the post. They are really helpful. I now learned makefile and the executables.
I installed the libreadline so.5 from Synaptic Package Manager in Ubuntu-64bit-11.04. After that the executable mothur worked as it should be.
By the way, I have another question. What’s the difference between CAP3 and Mothur when calculate OTUs? Does “distance = 0.10” in Mothur means 90% sequence similarity?
yes 10% distance/dissimilarity = 90% similarity in mothur, please feel free to start a new thread for this and other questions.