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install.sh
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install.sh
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#!/usr/bin/env bash
echo "#Installing MetaCompass"
cmd="g++ -Wall -W -O2 -o ./bin/extractSeq ./src/utils/extractSeq.cpp"
echo $cmd
$cmd
cmd="g++ -Wall -W -O2 -o ./bin/formatFASTA ./src/utils/formatFASTA.cpp"
echo $cmd
$cmd
cmd="g++ -Wall -W -O2 -o ./bin/buildcontig ./src/buildcontig/buildcontig.cpp ./src/buildcontig/cmdoptions.cpp ./src/buildcontig/memory.cpp ./src/buildcontig/procmaps.cpp ./src/buildcontig/outputfiles.cpp"
echo $cmd
$cmd
#wget https://gembox.cbcb.umd.edu/metacompass/refseq.tar.gz
#cd wgs-8.3rc2
#cd kmer && make install && cd ..
#cd src && make && cd ..
#cd ..
cmd="wget --no-check-certificate https://obj.umiacs.umd.edu/metacompass-treangen/markers.tar.gz -P ./src"
echo $cmd
$cmd
cmd="cd ./src/metaphyler/"
echo $cmd
$cmd
cmd="tar -xzvf ./markers.tar.gz"
echo $cmd
$cmd
cmd="cd ../../"
echo $cmd
$cmd
cmd="wget --no-check-certificate https://obj.umiacs.umd.edu/metacompass-treangen/refseq.tar.gz"
echo $cmd
$cmd
cmd="tar -xzvf refseq.tar.gz"
echo $cmd
$cmd
cmd="rm refseq.tar.gz"
#echo $cmd
$cmd