binaries/src/compilebin.sh

   1 #!/bin/bash
   2
   3 echo ""
   4 echo "Compiling Clustalw..."
   5 cd clustalw
   6 chmod +x ./configure
   7 ./configure
   8 make clean
   9 make
  10 chmod +x src/clustalw2
  11 cd ..
  12
  13 echo "Compiling Clustal Omega..."
  14 cd clustalo
  15 chmod +x ./configure
  16 ./configure
  17 make clean
  18 make
  19 chmod +x src/clustalo
  20 cd ..
  21
  22 echo "Compiling Mafft..."
  23 cd mafft/core
  24 make clean
  25 make
  26 cd ../..
  27
  28 echo "Compiling Mafft dependency fasta34..."
  29 cd fasta34
  30 rm *.o
  31 make
  32 chmod +x fasta34
  33 cd ..
  34
  35
  36 echo "Compiling Muscle..."
  37 cd muscle
  38 rm -f *.o muscle
  39 make
  40 cd ..
  41
  42 echo "Compiling Probcons..."
  43 cd probcons
  44 make clean
  45 make
  46 chmod +x probcons
  47 cd ..
  48
  49 echo "Compiling T-Coffee..."
  50 cd tcoffee
  51 chmod +x install
  52 ./install clean
  53 ./install t_coffee -force
  54 echo -e '#!/usr/bin/env bash\nPDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"\nexport PATH=$PATH:$PDIR\nt_coffee "$@"' > t_coffee_source/t_coffee.sh
  55 chmod +x t_coffee_source/t_coffee
  56 chmod +x t_coffee_source/t_coffee.sh
  57 cd ..
  58
  59 echo "Compiling DisEMBL..."
  60 cd disembl
  61 gcc -O3 disembl.c -o disembl
  62 echo "DONE"
  63 chmod +x disembl DisEMBL.py
  64
  65 echo "Compiling DisEMBL dependancy Tisean... "
  66 cd Tisean_3.0.1
  67 chmod +x ./configure
  68 ./configure
  69 make
  70 cp source_c/sav_gol ../
  71 cd ..
  72 echo "DONE"
  73 chmod +x sav_gol
  74 cd ..
  75
  76 echo "Setting up GlobPlot ..."
  77 cp disembl/sav_gol globplot/sav_gol
  78 cd globplot
  79 chmod +x GlobPlot.py
  80 echo "DONE"
  81 cd ..
  82
  83 echo "Compiling IUPred..."
  84 cd iupred
  85 make clean
  86 make
  87 echo "DONE"
  88 cd ..
  89
  90 echo "Compiling Vienna ..."
  91 cd ViennaRNA
  92 chmod +x ./configure
  93 ./configure
  94 make clean
  95 make
  96 echo "DONE"
  97 cd ..
  98
  99 echo "Compiling GLProbs ..."
 100 cd GLProbs-1.0
 101 make clean
 102 make
 103 echo "DONE"
 104 cd ..
 105
 106
 107 echo "Compiling MSAProbs-0.9.7 ..."
 108 cd MSAProbs-0.9.7/MSAProbs
 109 make clean
 110 make
 111 echo "DONE"
 112 cd ../..
 113