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1 #!/bin/bash
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2
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3 set -x
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4 set -eu
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5
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6 start_dir=$(pwd)
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7 ROARY_LIB_DIR="${start_dir}/lib"
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8 ROARY_BIN_DIR="${start_dir}/bin"
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9
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10 PARALLEL_VERSION=${PARALLEL_VERSION:-"20160722"}
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11 PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2"
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12 PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}"
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13
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14 BEDTOOLS_VERSION="2.27.1"
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15 BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz"
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16 BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}"
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17
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18 CDHIT_SHORT_VERSION="4.6.8"
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19 CDHIT_LONG_VERSION="4.6.8-2017-0621"
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20 CDHIT_DOWNLOAD_FILENAME="cd-hit-${CDHIT_SHORT_VERSION}.tar.gz"
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21 CDHIT_URL="https://github.com/weizhongli/cdhit/releases/download/V${CDHIT_SHORT_VERSION}/cd-hit-v${CDHIT_LONG_VERSION}-source.tar.gz"
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22
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23 PRANK_VERSION="0.140603"
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24 PRANK_DOWNLOAD_FILENAME="prank-msa-master.tar.gz"
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25 PRANK_URL="https://github.com/ariloytynoja/prank-msa/archive/master.tar.gz"
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26
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27 BLAST_VERSION="2.6.0"
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28 BLAST_DOWNLOAD_FILENAME="ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
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29 BLAST_URL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/${BLAST_DOWNLOAD_FILENAME}"
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30
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31 MCL_VERSION="14-137"
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32 MCL_DOWNLOAD_FILENAME="mcl-${MCL_VERSION}.tar.gz"
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33 MCL_URL="http://micans.org/mcl/src/mcl-${MCL_VERSION}.tar.gz"
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34
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35 FASTTREE_VERSION="2.1.10"
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36 FASTTREE_DOWNLOAD_FILENAME="FastTree-${FASTTREE_VERSION}.c"
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37 FASTTREE_URL="http://microbesonline.org/fasttree/FastTree-${FASTTREE_VERSION}.c"
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38
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39 MAFFT_VERSION="7.310"
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40 MAFFT_DOWNLOAD_FILENAME="mafft-${MAFFT_VERSION}-without-extensions-src.tgz"
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41 MAFFT_URL="http://mafft.cbrc.jp/alignment/software/${MAFFT_DOWNLOAD_FILENAME}"
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42
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43 # Make an install location
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44 if [ ! -d 'build' ]; then
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45 mkdir build
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46 fi
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47 cd build
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48 build_dir=$(pwd)
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49
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50 PARALLEL_DOWNLOAD_PATH="$(pwd)/${PARALLEL_DOWNLOAD_FILENAME}"
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51 BEDTOOLS_DOWNLOAD_PATH="$(pwd)/${BEDTOOLS_DOWNLOAD_FILENAME}"
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52 CDHIT_DOWNLOAD_PATH="$(pwd)/${CDHIT_DOWNLOAD_FILENAME}"
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53 PRANK_DOWNLOAD_PATH="$(pwd)/${PRANK_DOWNLOAD_FILENAME}"
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54 BLAST_DOWNLOAD_PATH="$(pwd)/${BLAST_DOWNLOAD_FILENAME}"
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55 MCL_DOWNLOAD_PATH="$(pwd)/${MCL_DOWNLOAD_FILENAME}"
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56 FASTTREE_DOWNLOAD_PATH="$(pwd)/${FASTTREE_DOWNLOAD_FILENAME}"
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57 MAFFT_DOWNLOAD_PATH="$(pwd)/${MAFFT_DOWNLOAD_FILENAME}"
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58
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59 PARALLEL_BUILD_DIR="$(pwd)/parallel-${PARALLEL_VERSION}"
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60 BEDTOOLS_BUILD_DIR="$(pwd)/bedtools2"
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61 CDHIT_BUILD_DIR="$(pwd)/cd-hit-v${CDHIT_LONG_VERSION}"
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62 PRANK_BUILD_DIR="$(pwd)/prank-msa-master"
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63 BLAST_BUILD_DIR="$(pwd)/ncbi-blast-${BLAST_VERSION}+"
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64 MCL_BUILD_DIR="$(pwd)/mcl-${MCL_VERSION}"
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65 FASTTREE_BUILD_DIR="$(pwd)/fasttree"
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66 MAFFT_BUILD_DIR="$(pwd)/mafft-${MAFFT_VERSION}-without-extensions"
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67
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68
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69 download () {
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70 download_url=$1
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71 download_path=$2
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72 cd $build_dir
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73 if [ -e "$download_path" ]; then
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74 echo "Skipping download of $download_url, $download_path already exists"
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75 else
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76 echo "Downloading $download_url to $download_path"
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77 wget $download_url -O $download_path
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78 pwd
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79 fi
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80 }
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81
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82 untar () {
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83 to_untar=$1
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84 expected_directory=$2
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85 if [ -d "$expected_directory" ]; then
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86 rm -rf $expected_directory
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87 fi
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88 echo "Untarring $to_untar to $expected_directory"
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89 cd $build_dir
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90 tar xzvf $to_untar
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91 rm $to_untar
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92 pwd
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93 }
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94
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95 if [ -e "$BLAST_BUILD_DIR/bin/blastp" ]; then
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96 echo "blast already untarred to $BLAST_BUILD_DIR, skipping"
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97 else
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98 download $BLAST_URL $BLAST_DOWNLOAD_PATH
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99 untar $BLAST_DOWNLOAD_PATH $BLAST_BUILD_DIR
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100 fi
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101
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102 # Build parallel
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103 if [ -e "$PARALLEL_BUILD_DIR/src/parallel" ]; then
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104 echo "Parallel already built, skipping"
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105 else
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106 download $PARALLEL_URL $PARALLEL_DOWNLOAD_PATH
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107 echo "Untarring parallel to $PARALLEL_BUILD_DIR"
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108 tar xjvf $PARALLEL_DOWNLOAD_PATH
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109 echo "Building parallel"
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110 cd $PARALLEL_BUILD_DIR
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111 ./configure
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112 make
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113 fi
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114
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115 # Build bedtools
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116 if [ -e "$BEDTOOLS_BUILD_DIR/bin/bedtools" ]; then
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117 echo "Bedtools already built, skipping"
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118 else
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119
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120 download $BEDTOOLS_URL $BEDTOOLS_DOWNLOAD_PATH
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121 untar $BEDTOOLS_DOWNLOAD_PATH $BEDTOOLS_BUILD_DIR
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122 cd $BEDTOOLS_BUILD_DIR
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123 echo "Building bedtools"
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124 ls -alrt
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125 make
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126 fi
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127
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128 # Build cd-hit
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129 if [ -e "$CDHIT_BUILD_DIR/cd-hit" ]; then
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130 echo "cd-hit already built, skipping"
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131 else
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132 download $CDHIT_URL $CDHIT_DOWNLOAD_PATH
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133 untar $CDHIT_DOWNLOAD_PATH $CDHIT_BUILD_DIR
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134 echo "Building cd-hit"
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135 cd $CDHIT_BUILD_DIR
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136 make
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137 fi
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138
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139 # Build prank
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140 if [ -e "$PRANK_BUILD_DIR/src/prank" ]; then
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141 echo "prank already built, skipping"
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142 else
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143 download $PRANK_URL $PRANK_DOWNLOAD_PATH
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144 untar $PRANK_DOWNLOAD_PATH $PRANK_BUILD_DIR
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145 echo "Building prank"
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146 cd $PRANK_BUILD_DIR
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147 cd src
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148 make
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149 fi
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150
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151 # Build MCL
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152 if [ -e "$MCL_BUILD_DIR/src/shmcl/mcl" ]; then
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153 echo "MCL already built, skipping"
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154 else
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155 download $MCL_URL $MCL_DOWNLOAD_PATH
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156 untar $MCL_DOWNLOAD_PATH $MCL_BUILD_DIR
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157 echo "Building MCL"
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158 cd $MCL_BUILD_DIR
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159 ./configure
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160 make
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161 fi
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162
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163 # Build FastTree
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164 if [ -e "$FASTTREE_BUILD_DIR/FastTree" ]; then
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165 echo "FastTree already built, skipping"
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166 else
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167 download $FASTTREE_URL $FASTTREE_DOWNLOAD_PATH
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168 mkdir -p $FASTTREE_BUILD_DIR
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169 mv $FASTTREE_DOWNLOAD_FILENAME $FASTTREE_BUILD_DIR
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170 cd $FASTTREE_BUILD_DIR
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171 echo "Building FastTree"
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172 gcc -o FastTree FastTree-${FASTTREE_VERSION}.c -lm
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173 fi
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174
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175 export MAFFT_INSTALL_DIR="${MAFFT_BUILD_DIR}/build"
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176 # Build MAFFT
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177 if [ -e "$MAFFT_BUILD_DIR/build/mafft" ]; then
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178 echo "MAFFT already built, skipping"
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179 else
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180 download $MAFFT_URL $MAFFT_DOWNLOAD_PATH
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181 untar $MAFFT_DOWNLOAD_PATH $MAFFT_BUILD_DIR
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182 echo "Building MAFFT"
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183 cd $MAFFT_BUILD_DIR
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184 mkdir -p $MAFFT_INSTALL_DIR
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185 cd core
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186 sed -i '1s!.*!PREFIX = $(MAFFT_INSTALL_DIR)!' Makefile
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187 make
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188 make install
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189 fi
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190
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191
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192 # Add things to PATH
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193 update_path () {
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194 new_dir=$1
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195 if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then
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196 echo "export PATH=${new_dir}:${PATH}"
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197 export PATH=${new_dir}:${PATH}
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198 fi
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199 }
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200
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201 export PATH
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202 PARALLEL_BIN_DIR="$PARALLEL_BUILD_DIR/src"
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203 update_path $PARALLEL_BIN_DIR
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204 BEDTOOLS_BIN_DIR="$BEDTOOLS_BUILD_DIR/bin"
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205 update_path $BEDTOOLS_BIN_DIR
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206 CDHIT_BIN_DIR="$CDHIT_BUILD_DIR"
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207 update_path $CDHIT_BIN_DIR
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208 PRANK_BIN_DIR="$PRANK_BUILD_DIR/src"
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209 update_path $PRANK_BIN_DIR
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210
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211 BLAST_BIN_DIR="$BLAST_BUILD_DIR/bin"
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212 update_path $BLAST_BIN_DIR
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213
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214 MCL_BIN_DIR="$MCL_BUILD_DIR/src/shmcl"
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215 update_path $MCL_BIN_DIR
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216 MCL_BIN_DIR_2="$MCL_BUILD_DIR/src/alien/oxygen/src"
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217 update_path $MCL_BIN_DIR_2
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218
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219 FASTTREE_BIN_DIR=$FASTTREE_BUILD_DIR
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220 update_path $FASTTREE_BIN_DIR
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221 MAFFT_BIN_DIR="$MAFFT_INSTALL_DIR/bin"
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222 update_path $MAFFT_BIN_DIR
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223
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224 update_perl_path () {
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225 new_dir=$1
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226 PERL5LIB=${PERL5LIB-$new_dir}
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227 if [[ ! "$PERL5LIB" =~ (^|:)"${new_dir}"(:|$) ]]; then
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228 echo "export PERL5LIB=${new_dir}:${PERL5LIB}"
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229 export PERL5LIB=${new_dir}:${PERL5LIB}
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230 fi
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231 }
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232
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233 BEDTOOLS_LIB_DIR="$BEDTOOLS_BUILD_DIR/lib"
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234 update_perl_path $BEDTOOLS_LIB_DIR
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235
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236 cd $start_dir
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237 cpanm --notest Dist::Zilla
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238 dzil authordeps --missing | cpanm --notest
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239 dzil listdeps --missing | cpanm --notest
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240
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241 cd $start_dir
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242
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243 echo "Add the following lines to one of these files ~/.bashrc or ~/.bash_profile or ~/.profile"
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244 echo "export PATH=${ROARY_BIN_DIR}:${PARALLEL_BIN_DIR}:${BEDTOOLS_BIN_DIR}:${CDHIT_BIN_DIR}:${PRANK_BIN_DIR}:${BLAST_BIN_DIR}:${MCL_BIN_DIR}:${MCL_BIN_DIR_2}:${FASTTREE_BIN_DIR}:${MAFFT_BIN_DIR}:${PATH}"
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245 echo "export PERL5LIB=${ROARY_LIB_DIR}:${BEDTOOLS_LIB_DIR}:${PERL5LIB}"
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246
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247 set +eu
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248 set +x
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