wget https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/download/builds/macosx_intel/v2.1.2/hapgen2_macosx_intel.tar.gz
tar zxvf hapgen2_macosx_intel.tar.gz
./hapgen2
if [ $? -eq 0 ] ; then
exit 0
else
exit 1
fi
[{ "name" : "exec",
"value" : "./hapgen2",
"description": "executable"}
]
wget https://mathgen.stats.ox.ac.uk/wtccc-software/HM3.tgz
tar zxvf HM3.tgz
command="./$md5checkdir__1__2__exec HM3/ 35f3dc6a51f47ade371e932ce275cc23"
eval $command
if [ $? -eq 0 ] ; then
exit 0
else
exit 1
fi
install_path = HM3/
wget http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip
unzip plink-1.07-x86_64.zip
cd plink-1.07-x86_64
./plink --noweb --file test
wget http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-mac-intel.zip
unzip plink-1.07-x86_64.zip
cd plink-1.07-mac-intel
./plink --noweb --file test
${output__result__extract_chromosome_from_ped__2}=${input__ped_map__extract_chromosome_from_ped__2}_chr_${input__chromosome__extract_chromosome_from_ped__2}
${plink__1_07__4__path} \
--noweb \
--file ${input__ped_map__extract_chromosome_from_ped__2} \
--chr ${input__chromosome__extract_chromosome_from_ped__2} \
--recode \
--out ${output__result__extract_chromosome_from_ped__2}
# Insert the BASH commands for this step
${input__chromosome__extract_chromosome_from_ped__3}="1"
${input__ped_map__extract_chromosome_from_ped__3}=${hapmap3__broad__1__path}
step__extract__extract_chromosome_from_ped__3
${output__hapmap3_chr1__hapmap2_chromosome_1__2}=${output__result__extract_chromosome_from_ped__3}
wget https://www.broadinstitute.org/files/shared/mpg/hapmap3/hapmap3_r1_b36_fwd_consensus.qc.poly.recode.map.bz2
bunzip2 hapmap3_r1_b36_fwd_consensus.qc.poly.recode.map.bz2
wget https://www.broadinstitute.org/files/shared/mpg/hapmap3/hapmap3_r1_b36_fwd_consensus.qc.poly.recode.ped.bz2
bunzip2 hapmap3_r1_b36_fwd_consensus.qc.poly.recode.ped.bz2
md5 -q hapmap3_r1_b36_fwd_consensus.qc.poly.recode.map | grep "688bbbc2a10ee8dbb3524f1121d045d1"
if [ $? -ne 0 ] ; then
exit 1
fi
md5 -q hapmap3_r1_b36_fwd_consensus.qc.poly.recode.ped | grep "1a2bce84f9fb3157875e049fe1830d85"
if [ $? -ne 0 ] ; then
exit 1
fi
exit 0