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#!/bin/sh
THIS_DIR=$(pwd)
mkdir $THIS_DIR/mafft_
tar -xvf mafft-6.240-src.tgz
cd mafft-6.240/src/
make clean
sed -i -e "s|PREFIX = /usr/local/lib/mafft|PREFIX = $THIS_DIR/mafft_|g" Makefile
make -j $NUM_CPU_JOBS
make install
cd ../..
cp -f mafft-6.240/scripts/mafft mafft_/
bunzip2 pyruvate_decarboxylase.fasta.bz2 -c > mafft_/pyruvate_decarboxylase.fasta
cat>align<<EOT
#!/bin/sh
cd mafft_/
./mafft --localpair --maxiterate 10000 pyruvate_decarboxylase.fasta 1>/dev/null 2>&1
cd ..
EOT
chmod +x align
cat>mafft<<EOT
#!/bin/sh
\$TIMER_START
./align 2>&1
\$TIMER_STOP
EOT
chmod +x mafft
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