config.site

#! /bin/sh

### This file is part of GMAP.  It allows you to provide values for
### the configuration process.  To set variables, uncomment the
### VAR=DEFAULT lines and set DEFAULT according to your needs.

########################################################################
### Configuration options
########################################################################

## The directory where the binary files will go (without the "/bin" at
## the end).  For example, if you want the gmap program to be
## installed as /usr/local/bin/gmap, the prefix is "/usr/local".  The
## directory must be an absolute path, so "." and "~" are not allowed.
##
## If you want to install in this build directory for testing purposes,
## specify prefix=`pwd` (with two backward quotes).  If you don't specify
## anything for prefix, it defaults to /usr/local.
##
## prefix=/usr/local


## The directory where the GMAP genome database files go.  Each genome
## must be set up (with the gmap_setup program) before gmap can map and
## align against that genome.  Each genome will get its own
## subdirectory in this directory.
##
## Note: at run time, the user may choose to override this directory
## by (1) providing a -D flag to gmap, (2) setting the GMAPDB
## environment variable, or (3) creating a configuration file .gmaprc
## with the line GMAPDB=<directory>.
##
## Make sure there is adequate disk space in this directory; for
## example, the human genome will need about 3 gigabytes.
##
## If you don't specify anything for with_gmapdb, it defaults to 
## ${prefix}/share.
##
## with_gmapdb=/path/to/gmapdb


## Popcnt support.  By default, the configure program will test your computer
## for popcnt and related commands (for fast bit counting), and if so, enable those
## commands to speed up the program.  If you plan to configure the package
## on one computer and then run the programs on another computer, you may
## need to disable this feature.  To disable the feature, specify --disable-popcnt
## or uncomment the line below and change the answer to "disable_popcnt".
##
## enable_popcnt


## SIMD support.  By default, the configure program will test your
## computer for SIMD commands (e.g., Intel SSE commands), and if so,
## enable those commands to speed up the program.  If you plan to
## configure the package on one computer and then run the programs on
## another computer, you may need to disable this feature.  To disable
## all SIMD support, specify --disable-simd or uncomment the line
## below and change the answer to "disable_simd".  Or you may disable
## individual types of SIMD commands, as listed below.
##
## enable_simd
## enable_sse2
## enable_sse4.1


## Optional zlib support (needed only for reading gzip-compressed files).  By
## default, the configure program will test to see if you have a
## working zlib library and if so, enable the feature.  If you want to
## disable the feature, specify --disable-zlib or uncomment the line
## below and change the answer to "disable_zlib".
##
## enable_zlib


## Optional bzlib support (needed only for reading bzip2-compressed files).  By
## default, the configure program will test to see if you have a
## working bzlib library and if so, enable the feature.  If you want to
## disable the feature, specify --disable-bzlib or uncomment the line
## below and change the answer to "disable_bzlib".
##
## enable_bzlib


## The command for the C compiler.  If unspecified, the GNU configure
## procedure will search for a suitable compiler, first for gcc and
## then for cc.  To override this choice, specify the name of your
## preferred C compiler here, for example, 'c89'.  
## CC=gcc
## or may want to specify another compiler
## CC=/usr/bin/cc


## Debugging and optimization options for the C compiler.  Use this to
## specify CFLAGS for the version of the C compiler specified above.
## If unspecified, defaults to '-O3' for fastest speed.  The configure
## script will also test whether -mpopcnt works and apply it if
## possible.  For Macintosh machines, you may need to add -m64 for
## the programs to work.
## CFLAGS='-O3'
## CFLAGS='-O3 -m64'   (for Macintosh machines)


## Debugging and optimization options for the MPICC compiler, used
## for the MPI versions of the programs.
## MPI_CFLAGS='-mpitrace'


## Search directory for header files ('-IDIR') and any other
## miscellaneous options for the C preprocessor and compiler.
## CPPFLAGS=-I/usr/local/include


## Path ('-L') and any other miscellaneous options for the linker.
## '-L' options set here will be prepended to LD_LIBRARY_PATH (or its
## system equivalent) at run time.
## For systems with shared libraries:
## LDFLAGS='-L/usr/local/lib -rpath /usr/local/lib'
## For most other systems, including the gcc compiler
## LDFLAGS='-L/usr/local/lib'


## Special flags (in addition to CFLAGS and LIBS) that may be needed
## for pthreads The configure program will attempt to determine these
## automatically, but will also try any flags you supply here.
## PTHREAD_CFLAGS=
## PTHREAD_LIBS=


## Make name.  Set this if you want to use a make by another name.
## For example, if your GNU make is called 'gmake', use 'MAKE=gmake'.
## MAKE=/usr/bin/make


## Location of Perl.  Some of the utility programs require Perl
## with working versions of IO::File and Getopt::Std.  The configure
## program will attempt to find a working version of Perl in your
## PATH, but you may need to or wish to specify a particular version
## of perl here, by providing its full path
## 
## PERL=/usr/local/bin/perl


## Maximum read length for GSNAP, defined at compile-time.  If this is
## not set here, then a default value of 250 will be used
##
## MAX_READLENGTH=250


## Header and library files for support of the external Goby library
##    from the Campagne lab at Cornell (optional)
## Requires the user to obtain and compile the libraries from
##    http://campagnelab.org/software/goby.
## Expects the header files to be in /path/to/goby/include and
##    the library files to be in /path/to/goby/lib
##
## with_goby=/path/to/goby