chmod +x src/clustalw2
cd ..
+echo "Compiling Clustal Omega..."
+cd clustalo
+chmod +x ./configure
+./configure
+make clean
+make
+chmod +x src/clustalo
+cd ..
+
echo "Compiling Mafft..."
cd mafft/core
make clean
make
-chmod +x mafft
cd ../..
-cd mafft/binaries
-chmod +x *
-cd ../..
-
echo "Compiling Mafft dependency fasta34..."
cd fasta34
echo "Compiling Muscle..."
cd muscle
-rm -f *.o
+rm -f *.o muscle
make
-chmod +x muscle
cd ..
echo "Compiling Probcons..."
./install clean
./install t_coffee -force
chmod +x t_coffee_source/t_coffee
+export PATH=$PATH:$PWD/t_coffee_source
cd ..
echo "Compiling DisEMBL..."
echo "Compiling DisEMBL dependancy Tisean... "
cd Tisean_3.0.1
+chmod +x ./configure
./configure
make
cp source_c/sav_gol ../
chmod +x sav_gol
cd ..
-echo "Compiling GlobPlot..."
+echo "Setting up GlobPlot ..."
+cp disembl/sav_gol globplot/sav_gol
cd globplot
-echo "DONE"
-# TODO deal with the links
chmod +x GlobPlot.py
+echo "DONE"
+cd ..
+
+echo "Compiling IUPred..."
+cd iupred
+make clean
+make
+echo "DONE"
+cd ..
+
+echo "Compiling Vienna ..."
+cd ViennaRNA
+chmod +x ./configure
+./configure
+make clean
+make
+echo "DONE"
+cd ..
+
+echo "Compiling GLProbs ..."
+cd GLProbs-1.0
+make clean
+make
+echo "DONE"
cd ..
+
+echo "Compiling MSAProbs-0.9.7 ..."
+cd MSAProbs-0.9.7/MSAProbs
+make clean
+make
+echo "DONE"
+cd ../..
+