# Makefile options

OPTIMIZE ?= yes
USEBOOST ?= no
USEHDF5 ?= no
USEGSL ?= no
LOGFILE_NAME ?= no
VERSION = ""1.44.0""


## Optimize

The optimize option will include the -O3 compile flag. The -O3 flag adds compile time, but reduces execution time and code size.

OPTIMIZE ?= yes

ifeq  ($(strip$(OPTIMIZE)),yes)
CXXFLAGS += -O3
endif


## Setting a default location

You can set a default location for mothur to look for input files, if they are not found. This will allow you to keep your reference files in one location and save time typing lengthy filenames. This location can be overridden using the set.dir command at run time.

To do this: change Enter_your_default_path_here to the location you would like to use as a default. For example let’s set my default to the release folder on my desktop:

MOTHUR_FILES = "/Users/sarahwestcott/desktop/release"

ifeq  ($(strip$(MOTHUR_FILES)),""Enter_your_default_path_here"")
else
CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES} endif  To clear this at run time: mothur > set.dir(tempdefault=clear)  or to set it to another location: mothur > set.dir(tempdefault=/Users/sarahwestcott/desktop/MiSeq_SOP)  ## Set location for mothur’s external tools The mothur tools option can be used to set a default location for mothur’s external tools. For example, you might install vsearch, uchime, prefetch and fasterq-dump in a central location like /usr/bin, and indicate to mothur to look there: MOTHUR_TOOLS="/usr/bin" ifeq ($(strip $(MOTHUR_TOOLS)),""Enter_your_mothur_tools_path_here"") else CXXFLAGS += -DMOTHUR_TOOLS=${MOTHUR_TOOLS}
endif


You can set this location at run time using the set.dir command:

mothur > set.dir(tools=/usr/bin)


## Set static logfile name

By default mothur will create a logfile for each run of mothur. The default log file name is mothur.XXX.logfile, where XXX is the time and date stamp. These logs can quickly add up. To set a static logfile name that will be overwritten with each run of mothur try the following:

LOGFILE_NAME ?=yes

ifeq  ($(strip$(LOGFILE_NAME)),yes)
LOGFILE_NAME=""mothur.logfile""
endif


To silence the log feature compile with the name set to silent:

ifeq  ($(strip$(LOGFILE_NAME)),yes)
LOGFILE_NAME=""silent""
endif


To set the log file name at run time:

mothur > set.logfile(name=my.mothur.log)


The readline library is not required to run mothur, but it will allow you to scroll through the commands you have entered if you are running mothur in interactive mode. If you do not want to use the readline library, change the yes to no below. If you are going to use it, make sure you have the readline library and ncurses library installed on your machine.

 USEREADLINE ?= yes

ifeq  ($(strip$(USEREADLINE)),yes)
LDFLAGS += \
-lncurses
endif


## Boost Libraries

The boost libraries allow the make.contigs command to read *.gz files. This is not required, but many users find it helpful. If you do not want to use the boost libraries, simply change the yes to no below. If you are going to use it, make sure you have the boost libraries installed on your machine, and set the boost locations. For example, I installed the boost libraries in /usr/local/lib with the include headers in /usr/local/include:

USEBOOST ?= yes
BOOST_INCLUDE_DIR="/usr/local/include"
BOOST_LIBRARY_DIR="/usr/local/lib"

ifeq  ($(strip$(USEBOOST)),yes)

LDFLAGS += -L ${BOOST_LIBRARY_DIR} LIBS += -lboost_iostreams -lz CXXFLAGS += -DUSE_BOOST -I${BOOST_INCLUDE_DIR}
endif


## HDF5 Libraries

The HDF5 libraries allow the biom.info command to read biom files in HDF5 format. This is not required. If you do not want to use the hdf5 libraries, simply change the yes to no below. If you are going to use it, make sure you have the hdf5 libraries installed on your machine, and set the hdf5 locations. For example, I installed the hdf5 libraries in /usr/local/lib with the include headers in /usr/local/include:

USEHDF5 ?= yes
HDF5_INCLUDE_DIR="/usr/local/include"
HDF5_LIBRARY_DIR="/usr/local/lib"

ifeq  ($(strip$(USEHDF5)),yes)

LDFLAGS += -L ${HDF5_LIBRARY_DIR} LIBS += -lhdf5 -lhdf5_cpp CXXFLAGS += -DUSE_HDF5 -I${HDF5_INCLUDE_DIR}

endif


## GSL Libraries

The GSL libraries allow the estimator.single command. This is not required. If you do not want to use the estimator.single command, simply change the yes to no below. If you are going to use it, make sure you have the GSL libraries installed on your machine, and set the GSL locations. For example, I installed the GSL libraries in /usr/local/gsl/lib with the include headers in /usr/local/gsl/include:

USEGSL ?= yes
GSL_LIBRARY_DIR ?= ""/usr/local/gsl/lib""
GSL_INCLUDE_DIR ?= ""/usr/local/gsl/include""

ifeq  ($(strip$(USEGSL)),yes)

LDFLAGS += -L ${GSL_LIBRARY_DIR} LIBS += -lgsl -lgslcblas -lm CXXFLAGS += -DUSE_GSL -I${GSL_INCLUDE_DIR}

endif