INSTALL

Note that for GD you may need this library: libgd-dev
$ sudo apt-get install libgd-dev

We use CPANm to install Perl libraries
$ sudo apt-get install cpanm

Then you need to install some Perl libraries. This can be done by your system administrator or in your own user directory (if setup properly - ask your sysadmin)

$ sudo ./dew.install.sh

==Errors from other people
======================================================================================
There seems to be an issue with the Bio::Graphics library. In particular the file Bio/Graphics/Glyph/xyplot.pm
If you are having issues, after you install Bio::Graphics do (as root or sudo unless you installed Bio/Graphics as a user)
updatedb && locate Bio/Graphics/Glyph/xyplot.pm
patch Bio/Graphics/Glyph/xyplot.pm patch.biographics.diff

This fixes a fatal error when trying to make SVG XY plot graphics 


== For people using intel compilers:
======================================================================================
Some software have issues when installing with intel's compiler ICC. 
For that reason, before running make you may need to force the GCC compiler like so:
export CC=`which gcc` # if which returns a path directly e.g. '/usr/bin/gcc'
export CC=`which -p gcc` # if which returns 'gcc is /usr/bin/gcc'
export CXX=`which g++`
export CXX=`which -p g++`

DO the above if make fails (don't forget to run make clean)

For Samtools, you need this:
export CPPFLAGS="$CPPFLAGS -fopenmp"
export LIBPATH=$LDFLAGS
export LDFLAGS="$LDFLAGS -fopenmp"

Then Samtools requires editing the various Makefiles if you have custom library paths (add $(LDFLAGS) in the CFLAGS lines )
e.g. bcftools/Makefile
before: CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
after: CFLAGS= -g -Wall -O2 $(LDFLAGS) #-m64 #-arch ppc

======================================================================================