X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=binaries%2Fsrc%2Fcompilebin.sh;h=87ce823e336c6da47cd2d9fa83f988231af9adcb;hb=d33d2debf752b2b31d5a801eb93eaa3f5ce23028;hp=c530cca5915842d9f972a3286d200ac9f67e649c;hpb=1e29b6fbcedf82cadc24953888a86451b2b86452;p=jabaws.git

diff --git a/binaries/src/compilebin.sh b/binaries/src/compilebin.sh
old mode 100644
new mode 100755
index c530cca..87ce823
--- a/binaries/src/compilebin.sh
+++ b/binaries/src/compilebin.sh
@@ -10,6 +10,14 @@ make
 chmod +x src/clustalw2 
 cd ..
 
+echo "Compiling Clustal Omega..."
+cd clustalo
+make clean
+chmod +x ./configure 
+./configure
+make
+cd ..
+
 echo "Compiling Mafft..."
 cd mafft/core
 make clean
@@ -26,9 +34,8 @@ cd ..
 
 echo "Compiling Muscle..."
 cd muscle
-rm -f *.o
+rm -f *.o muscle
 make
-chmod +x muscle
 cd ..
 
 echo "Compiling Probcons..."
@@ -54,6 +61,7 @@ chmod +x disembl DisEMBL.py
 
 echo "Compiling DisEMBL dependancy Tisean... "
 cd Tisean_3.0.1
+chmod +x ./configure
 ./configure
 make
 cp source_c/sav_gol ../
@@ -62,12 +70,11 @@ echo "DONE"
 chmod +x sav_gol
 cd ..
 
-# TODO copy sav_gol other from disembl
-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..."
@@ -77,3 +84,12 @@ make
 echo "DONE"
 cd ..
 
+echo "Compiling Vienna ..."
+cd ViennaRNA
+chmod +x ./configure
+./configure
+make clean
+make
+echo "DONE"
+cd ..
+