 
!!!!!! REMEMBER TO CHANGE VERSION NUMBER IN data.h !!!!!
// Mac Leopard + Tiger

make clean
make -f Makefile.mac
tar cvzf impute_v1.0.0_MacOSX_Intel.tgz impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_MacOSX_Intel.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// Mac PPC

ssh neandertal.bscb.cornell.edu 
make clean
make -f Makefile.dynamic
tar cvzf impute_v1.0.0_MacOSX_PowerPC.tgz impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_MacOSX_PowerPC.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// x86_64 (teal)

make clean
make
tar cvzf impute_v1.0.0_x86_64_static.tgz impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_x86_64_static.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

make clean
make -f Makefile.dynamic
tar cvzf impute_v1.0.0_x86_64_dynamic.tgz impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_x86_64_dynamic.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// i386 (blackcap)

make clean
make
tar cvzf impute_v1.0.0_i386_static.tgz impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_i386_static.tgz  blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

make clean
make -f Makefile.dynamic
tar cvzf impute_v1.0.0_i386_dynamic.tgz impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_i386_dynamic.tgz  blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// Solaris 5.8 SPARC (markov)

/usr/local/bin/gmake -f Makefile.solaris clean
/usr/local/bin/gmake -f Makefile.solaris
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
tar cvf impute_v1.0.0_Solaris5.8_SPARC.tar  impute example/* LICENCE
gzip  impute_v1.0.0_Solaris5.8_SPARC.tar
scp impute_v1.0.0_Solaris5.8_SPARC.tar.gz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// Solaris 5.10 Opteron (blackhawk)

/opt/csw/bin/gmake -f Makefile.solaris.blackhawk clean
/opt/csw/bin/gmake -f Makefile.solaris.blackhawk
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
tar cvf impute_v1.0.0_Solaris5.10_Opteron.tar  impute example/* LICENCE
gzip  impute_v1.0.0_Solaris5.10_Opteron.tar
scp  impute_v1.0.0_Solaris5.10_Opteron.tar.gz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// SLES 10 (Intel Itanium2)
ssh orac.osc.ox.ac.uk
make clean
make -f Makefile.orac
tar cvzf impute_v1.0.0_SLES10_Itanium2.tgz  impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_SLES10_Itanium2.tgz gate.stats.ox.ac.uk:~/


// x86_64 SuSE9.3 (genecluster)
make clean
make 
tar cvzf impute_v1.0.0_SuSE9.3_x86_64_static.tgz  impute example/* LICENCE
./impute -h example/haplo.txt -l example/legend.txt -g example/geno.txt -m example/map.txt -s example/strand.txt -Ne 11400 -int 62000000 63000000
scp impute_v1.0.0_SuSE9.3_x86_64_static.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute



// Windows

make -f Makefile.win
tar cvzf impute_v1.0.0_Windows_Intel.tgz  impute.exe zlibwapi.dll example/* LICENCE



// VERSION 2

// Mac Leopard

make clean
make -f Makefile.mac
./impute2 -m ./Example/example.chr22.map  -h ./Example/example.chr22.1kG.haps ./Example/example.chr22.hm3.haps -l ./Example/example.chr22.1kG.legend ./Example/example.chr22.hm3.legend -g ./Example/example.chr22.study.gens -strand_g ./Example/example.chr22.study.strand -int 20.4e6 20.5e6 -Ne 11418 -o ./Example/example.chr22.two.phased.impute2
rm ./Example/example.chr22.two.phased.impute2*

mkdir impute_v2.1.2_MacOSX_Intel
mkdir impute_v2.1.2_MacOSX_Intel/Example
cp -rf impute2 LICENCE impute_v2.1.2_MacOSX_Intel
cp Example/*.* impute_v2.1.2_MacOSX_Intel/Example/
tar cvzf impute_v2.1.2_MacOSX_Intel.tgz impute_v2.1.2_MacOSX_Intel

scp impute_v2.1.2_MacOSX_Intel.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute


// x86_64 dynamic (teal)

make clean
make
./impute2 -m ./Example/example.chr22.map  -h ./Example/example.chr22.1kG.haps ./Example/example.chr22.hm3.haps -l ./Example/example.chr22.1kG.legend ./Example/example.chr22.hm3.legend -g ./Example/example.chr22.study.gens -strand_g ./Example/example.chr22.study.strand -int 20.4e6 20.5e6 -Ne 11418 -o ./Example/example.chr22.two.phased.impute2

rm ./Example/example.chr22.two.phased.impute2*

mkdir impute_v2.1.2_x86_64_dynamic
mkdir impute_v2.1.2_x86_64_dynamic/Example
cp -rf impute2 LICENCE impute_v2.1.2_x86_64_dynamic
cp Example/*.* impute_v2.1.2_x86_64_dynamic/Example/
tar cvzf impute_v2.1.2_x86_64_dynamic.tgz impute_v2.1.2_x86_64_dynamic

scp impute_v2.1.2_x86_64_dynamic.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute

// x86_64 static (wattle)

make clean
make -f Makefile.static
./impute2 -m ./Example/example.chr22.map  -h ./Example/example.chr22.1kG.haps ./Example/example.chr22.hm3.haps -l ./Example/example.chr22.1kG.legend ./Example/example.chr22.hm3.legend -g ./Example/example.chr22.study.gens -strand_g ./Example/example.chr22.study.strand -int 20.4e6 20.5e6 -Ne 11418 -o ./Example/example.chr22.two.phased.impute2

rm ./Example/example.chr22.two.phased.impute2*

mkdir impute_v2.1.2_x86_64_static
mkdir impute_v2.1.2_x86_64_static/Example
cp -rf impute2 LICENCE impute_v2.1.2_x86_64_static
cp Example/*.* impute_v2.1.2_x86_64_static/Example/
tar cvzf impute_v2.1.2_x86_64_static.tgz impute_v2.1.2_x86_64_static

scp impute_v2.1.2_x86_64_static.tgz gate.stats.ox.ac.uk:~/


// x86_64 (genecluster)

make clean
make

./impute2 -m ./Example/example.chr22.map  -h ./Example/example.chr22.1kG.haps ./Example/example.chr22.hm3.haps -l ./Example/example.chr22.1kG.legend ./Example/example.chr22.hm3.legend -g ./Example/example.chr22.study.gens -strand_g ./Example/example.chr22.study.strand -int 20.4e6 20.5e6 -Ne 11418 -o ./Example/example.chr22.two.phased.impute2

rm ./Example/example.chr22.two.phased.impute2*

mkdir impute_v2.1.2_SuSE9.3_x86_64_static
mkdir impute_v2.1.2_SuSE9.3_x86_64_static/Example
cp -rf impute2 LICENCE impute_v2.1.2_SuSE9.3_x86_64_static
cp Example/*.* impute_v2.1.2_SuSE9.3_x86_64_static/Example/
tar cvzf impute_v2.1.2_SuSE9.3_x86_64_static.tgz impute_v2.1.2_SuSE9.3_x86_64_static

scp impute_v2.1.2_SuSE9.3_x86_64_static.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute


// Solaris 5.10 Opteron (blackhawk)

/opt/csw/bin/gmake -f Makefile.solaris.blackhawk clean
/opt/csw/bin/gmake -f Makefile.solaris.blackhawk


./impute2 -m ./Example/example.chr22.map  -h ./Example/example.chr22.1kG.haps ./Example/example.chr22.hm3.haps -l ./Example/example.chr22.1kG.legend ./Example/example.chr22.hm3.legend -g ./Example/example.chr22.study.gens -strand_g ./Example/example.chr22.study.strand -int 20.4e6 20.5e6 -Ne 11418 -o ./Example/example.chr22.two.phased.impute2

rm ./Example/example.chr22.two.phased.impute2*

mkdir impute_v2.1.2_Solaris5.10_Opteron
mkdir impute_v2.1.2_Solaris5.10_Opteron/Example
cp -rf impute2 LICENCE impute_v2.1.2_Solaris5.10_Opteron
cp Example/*.* impute_v2.1.2_Solaris5.10_Opteron/Example/
tar cvf impute_v2.1.2_Solaris5.10_Opteron.tar impute_v2.1.2_Solaris5.10_Opteron
gzip impute_v2.1.2_Solaris5.10_Opteron.tar

scp impute_v2.1.2_Solaris5.10_Opteron.tar.gz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute


// i386 (zeon)

make clean
make

./impute2 -m ./Example/example.chr22.map  -h ./Example/example.chr22.1kG.haps ./Example/example.chr22.hm3.haps -l ./Example/example.chr22.1kG.legend ./Example/example.chr22.hm3.legend -g ./Example/example.chr22.study.gens -strand_g ./Example/example.chr22.study.strand -int 20.4e6 20.5e6 -Ne 11418 -o ./Example/example.chr22.two.phased.impute2


rm ./Example/example.chr22.two.phased.impute2*

mkdir impute_v2.1.2_i386_dynamic
mkdir impute_v2.1.2_i386_dynamic/Example
cp -rf impute2 LICENCE impute_v2.1.2_i386_dynamic
cp Example/*.* impute_v2.1.2_i386_dynamic/Example/
tar cvzf impute_v2.1.2_i386_dynamic.tgz impute_v2.1.2_i386_dynamic

scp impute_v2.1.2_i386_dynamic.tgz gate.stats.ox.ac.uk:~/



tar cvzf impute_v2.0.4_i386_dynamic.tgz impute2 Example/*.*  LICENCE
scp impute_v2.0.4_i386_dynamic.tgz blacktern.stats.ox.ac.uk:/data/sites/mathgen/htdocs/impute




// Mac PowerPC

ssh neandertal.bscb.cornell.edu 

make clean
make -f Makefile.dynamic
./impute2 -m ./Example/chr16.map -g_ref ./Example/chr16.reference.gtypes -s_ref ./Example/chr16.reference.strand -g ./Example/chr16.study.gtypes -s ./Example/chr16.study.strand -Ne 11418 -int 5000000 5500000 -buffer 250 -k 10 -iter 10 -burnin 3 -o ./Example/Results/chr16.diploid_panel.impute2 -i ./Example/Results/chr16.diploid_panel.impute2.info -r ./Example/Results/chr16.diploid_panel.impute2.summary
rm ./Example/Results/*
tar cvzf impute_v2.0.4_MacOSX_PowerPC.tgz impute2 Example/*.*  LICENCE
scp impute_v2.0.4_MacOSX_PowerPC.tgz gate.stats.ox.ac.uk:~/





// SLES 10 (Intel Itanium2)
ssh orac.osc.ox.ac.uk
make clean
make -f Makefile.orac

./impute2 -m ./Example/chr16.map -g_ref ./Example/chr16.reference.gtypes -s_ref ./Example/chr16.reference.strand -g ./Example/chr16.study.gtypes -s ./Example/chr16.study.strand -Ne 11418 -int 5000000 5500000 -buffer 250 -k 10 -iter 10 -burnin 3 -o ./Example/Results/chr16.diploid_panel.impute2 -i ./Example/Results/chr16.diploid_panel.impute2.info -r ./Example/Results/chr16.diploid_panel.impute2.summary
rm ./Example/Results/*

tar cvzf impute_v2.0.4_SLES10_Itanium2.tgz impute2 Example/*.*  LICENCE
scp impute_v2.0.4_SLES10_Itanium2.tgz gate.stats.ox.ac.uk:~/


