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41
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1 #!/bin/sh -e
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2 #
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3 # Prototype script to setup a conda environment with the
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4 # dependencies needed for the Amplicon_analysis_pipeline
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5 # script
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6 #
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7 # Handle command line
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8 usage()
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9 {
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10 echo "Usage: $(basename $0) [DIR]"
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11 echo ""
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12 echo "Installs the Amplicon_analysis_pipeline package plus"
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13 echo "dependencies in directory DIR (or current directory "
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14 echo "if DIR not supplied)"
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15 }
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16 if [ ! -z "$1" ] ; then
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17 # Check if help was requested
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18 case "$1" in
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19 --help|-h)
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20 usage
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21 exit 0
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22 ;;
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23 esac
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24 # Assume it's the installation directory
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25 cd $1
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26 fi
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27 # Versions
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28 PIPELINE_VERSION=1.2.3
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29 RDP_CLASSIFIER_VERSION=2.2
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30 # Directories
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31 TOP_DIR=$(pwd)/Amplicon_analysis-${PIPELINE_VERSION}
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32 BIN_DIR=${TOP_DIR}/bin
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33 CONDA_DIR=${TOP_DIR}/conda
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34 CONDA_BIN=${CONDA_DIR}/bin
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35 CONDA_LIB=${CONDA_DIR}/lib
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36 CONDA=${CONDA_BIN}/conda
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37 ENV_NAME="amplicon_analysis_pipeline@${PIPELINE_VERSION}"
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38 ENV_DIR=${CONDA_DIR}/envs/$ENV_NAME
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39 #
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40 # Functions
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41 #
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42 # Report failure and terminate script
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43 fail()
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44 {
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45 echo ""
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46 echo ERROR $@ >&2
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47 echo ""
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48 echo "$(basename $0): installation failed"
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49 exit 1
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50 }
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51 #
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52 # Rewrite the shebangs in the installed conda scripts
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53 # to remove the full path to conda 'bin' directory
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54 rewrite_conda_shebangs()
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55 {
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56 pattern="s,^#!${CONDA_BIN}/,#!/usr/bin/env ,g"
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57 find ${CONDA_BIN} -type f -exec sed -i "$pattern" {} \;
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58 }
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59 #
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60 # Install conda
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61 install_conda()
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62 {
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63 echo "++++++++++++++++"
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64 echo "Installing conda"
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65 echo "++++++++++++++++"
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66 if [ -e ${CONDA_DIR} ] ; then
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67 echo "*** $CONDA_DIR already exists ***" >&2
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68 return
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69 fi
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70 local cwd=$(pwd)
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71 local wd=$(mktemp -d)
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72 cd $wd
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73 wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
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74 bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
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75 echo Installed conda in ${CONDA_DIR}
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76 # Update the installation files
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77 # This is to avoid problems when the length the installation
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78 # directory path exceeds the limit for the shebang statement
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79 # in the conda files
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80 echo ""
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81 echo -n "Rewriting conda shebangs..."
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82 rewrite_conda_shebangs
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83 echo "ok"
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84 echo -n "Adding conda bin to PATH..."
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85 PATH=${CONDA_BIN}:$PATH
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86 echo "ok"
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87 cd $cwd
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88 rm -rf $wd/*
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89 rmdir $wd
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90 }
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91 #
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92 # Create conda environment
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93 install_conda_packages()
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94 {
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95 echo "+++++++++++++++++++++++++"
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96 echo "Installing conda packages"
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97 echo "+++++++++++++++++++++++++"
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98 local cwd=$(pwd)
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99 local wd=$(mktemp -d)
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100 cd $wd
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101 cat >environment.yml <<EOF
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102 name: ${ENV_NAME}
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103 channels:
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104 - defaults
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105 - conda-forge
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106 - bioconda
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107 dependencies:
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108 - python=2.7
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109 - cutadapt=1.11
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110 - sickle-trim=1.33
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111 - bioawk=1.0
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112 - pandaseq=2.8.1
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113 - spades=3.5.0
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114 - fastqc=0.11.3
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115 - qiime=1.8.0
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116 - blast-legacy=2.2.26
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117 - fasta-splitter=0.2.4
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118 - rdp_classifier=$RDP_CLASSIFIER_VERSION
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119 - vsearch=1.1.3
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120 # Need to explicitly specify libgfortran
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121 # version (otherwise get version incompatible
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122 # with numpy=1.7.1)
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123 - libgfortran=1.0
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124 # Compilers needed to build R
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125 - gcc_linux-64
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126 - gxx_linux-64
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127 - gfortran_linux-64
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128 EOF
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129 ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
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130 echo Created conda environment in ${ENV_DIR}
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131 cd $cwd
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132 rm -rf $wd/*
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133 rmdir $wd
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134 }
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135 #
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136 # Install all the non-conda dependencies in a single
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137 # function (invokes separate functions for each package)
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138 install_non_conda_packages()
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139 {
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140 echo "+++++++++++++++++++++++++++++"
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141 echo "Installing non-conda packages"
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142 echo "+++++++++++++++++++++++++++++"
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143 # Temporary working directory
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144 local wd=$(mktemp -d)
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145 local cwd=$(pwd)
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146 local wd=$(mktemp -d)
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147 cd $wd
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148 # Amplicon analysis pipeline
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149 echo -n "Installing Amplicon_analysis_pipeline..."
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150 if [ -e ${BIN_DIR}/Amplicon_analysis_pipeline.sh ] ; then
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151 echo "already installed"
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152 else
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153 install_amplicon_analysis_pipeline
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154 echo "ok"
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155 fi
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156 # ChimeraSlayer
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157 echo -n "Installing ChimeraSlayer..."
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158 if [ -e ${BIN_DIR}/ChimeraSlayer.pl ] ; then
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159 echo "already installed"
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160 else
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161 install_chimeraslayer
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162 echo "ok"
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163 fi
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164 # Uclust
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165 echo -n "Installing uclust for QIIME/pyNAST..."
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166 if [ -e ${BIN_DIR}/uclust ] ; then
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167 echo "already installed"
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168 else
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169 install_uclust
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170 echo "ok"
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171 fi
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172 # R 3.2.1"
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173 echo -n "Checking for R 3.2.1..."
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174 if [ -e ${BIN_DIR}/R ] ; then
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175 echo "R already installed"
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176 else
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177 echo "not found"
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178 install_R_3_2_1
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179 fi
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180 }
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181 #
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182 # Amplicon analyis pipeline
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183 install_amplicon_analysis_pipeline()
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184 {
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185 local wd=$(mktemp -d)
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186 local cwd=$(pwd)
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187 local wd=$(mktemp -d)
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188 cd $wd
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189 wget -q https://github.com/MTutino/Amplicon_analysis/archive/v${PIPELINE_VERSION}.tar.gz
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190 tar zxf v${PIPELINE_VERSION}.tar.gz
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191 cd Amplicon_analysis-${PIPELINE_VERSION}
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192 INSTALL_DIR=${TOP_DIR}/share/amplicon_analysis_pipeline-${PIPELINE_VERSION}
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193 mkdir -p $INSTALL_DIR
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194 ln -s $INSTALL_DIR ${TOP_DIR}/share/amplicon_analysis_pipeline
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195 for f in *.sh ; do
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196 /bin/cp $f $INSTALL_DIR
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197 done
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198 /bin/cp -r uc2otutab $INSTALL_DIR
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199 mkdir -p ${BIN_DIR}
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200 cat >${BIN_DIR}/Amplicon_analysis_pipeline.sh <<EOF
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201 #!/usr/bin/env bash
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202 #
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203 # Point to Qiime config
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204 export QIIME_CONFIG_FP=${TOP_DIR}/qiime/qiime_config
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205 # Set up the RDP jar file
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206 export RDP_JAR_PATH=${TOP_DIR}/share/rdp_classifier/rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
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207 # Put the scripts onto the PATH
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208 export PATH=${BIN_DIR}:${INSTALL_DIR}:\$PATH
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209 # Activate the conda environment
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210 export PATH=${CONDA_BIN}:\$PATH
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211 source ${CONDA_BIN}/activate ${ENV_NAME}
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212 # Execute the driver script with the supplied arguments
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213 $INSTALL_DIR/Amplicon_analysis_pipeline.sh \$@
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214 exit \$?
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215 EOF
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216 chmod 0755 ${BIN_DIR}/Amplicon_analysis_pipeline.sh
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217 cat >${BIN_DIR}/install_reference_data.sh <<EOF
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218 #!/usr/bin/env bash -e
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219 #
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220 function usage() {
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221 echo "Usage: \$(basename \$0) DIR"
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222 }
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223 if [ -z "\$1" ] ; then
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224 usage
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225 exit 0
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226 elif [ "\$1" == "--help" ] || [ "\$1" == "-h" ] ; then
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227 usage
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228 echo ""
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229 echo "Install reference data into DIR"
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230 exit 0
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231 fi
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232 echo "=========================================="
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233 echo "Installing Amplicon analysis pipeline data"
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234 echo "=========================================="
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235 if [ ! -e "\$1" ] ; then
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236 echo "Making directory \$1"
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237 mkdir -p \$1
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238 fi
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239 cd \$1
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240 DATA_DIR=\$(pwd)
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241 echo "Installing reference data under \$DATA_DIR"
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242 $INSTALL_DIR/References.sh
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243 echo ""
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244 echo "Use '-r \$DATA_DIR' when running Amplicon_analysis_pipeline.sh"
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245 echo "to use the reference data from this directory"
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246 echo ""
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247 echo "\$(basename \$0): finished"
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248 EOF
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249 chmod 0755 ${BIN_DIR}/install_reference_data.sh
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250 cd $cwd
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251 rm -rf $wd/*
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252 rmdir $wd
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253 }
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254 #
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255 # ChimeraSlayer
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256 install_chimeraslayer()
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257 {
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258 local cwd=$(pwd)
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259 local wd=$(mktemp -d)
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260 cd $wd
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261 wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
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262 tar zxf microbiomeutil_2010-04-29.tar.gz
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263 cd microbiomeutil_2010-04-29
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264 INSTALL_DIR=${TOP_DIR}/share/microbiome_chimeraslayer-2010-04-29
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265 mkdir -p $INSTALL_DIR
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266 ln -s $INSTALL_DIR ${TOP_DIR}/share/microbiome_chimeraslayer
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267 /bin/cp -r ChimeraSlayer $INSTALL_DIR
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268 cat >${BIN_DIR}/ChimeraSlayer.pl <<EOF
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269 #!/usr/bin/env bash
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270 export PATH=$INSTALL_DIR:\$PATH
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271 $INSTALL_DIR/ChimeraSlayer/ChimeraSlayer.pl $@
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272 EOF
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273 chmod 0755 ${INSTALL_DIR}/ChimeraSlayer/ChimeraSlayer.pl
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274 chmod 0755 ${BIN_DIR}/ChimeraSlayer.pl
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275 cd $cwd
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276 rm -rf $wd/*
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277 rmdir $wd
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278 }
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279 #
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280 # uclust required for QIIME/pyNAST
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281 # License only allows this version to be used with those two packages
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282 # See: http://drive5.com/uclust/downloads1_2_22q.html
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283 install_uclust()
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284 {
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285 local wd=$(mktemp -d)
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286 local cwd=$(pwd)
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287 local wd=$(mktemp -d)
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288 cd $wd
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289 wget -q http://drive5.com/uclust/uclustq1.2.22_i86linux64
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290 INSTALL_DIR=${TOP_DIR}/share/uclust-1.2.22
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291 mkdir -p $INSTALL_DIR
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292 ln -s $INSTALL_DIR ${TOP_DIR}/share/uclust
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293 /bin/mv uclustq1.2.22_i86linux64 ${INSTALL_DIR}/uclust
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294 chmod 0755 ${INSTALL_DIR}/uclust
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295 ln -s ${INSTALL_DIR}/uclust ${BIN_DIR}
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296 cd $cwd
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297 rm -rf $wd/*
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298 rmdir $wd
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299 }
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300 #
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301 # R 3.2.1
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302 # Can't use version from conda due to dependency conflicts
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303 install_R_3_2_1()
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304 {
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305 . ${CONDA_BIN}/activate ${ENV_NAME}
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306 local cwd=$(pwd)
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307 local wd=$(mktemp -d)
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308 cd $wd
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309 echo -n "Fetching R 3.2.1 source code..."
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310 wget -q http://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz
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311 echo "ok"
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312 INSTALL_DIR=${TOP_DIR}
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313 mkdir -p $INSTALL_DIR
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314 echo -n "Unpacking source code..."
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315 tar xzf R-3.2.1.tar.gz >INSTALL.log 2>&1
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316 echo "ok"
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317 cd R-3.2.1
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318 echo -n "Running configure..."
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319 ./configure --prefix=$INSTALL_DIR --with-x=no --with-readline=no >>INSTALL.log 2>&1
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320 echo "ok"
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321 echo -n "Running make..."
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322 make >>INSTALL.log 2>&1
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323 echo "ok"
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324 echo -n "Running make install..."
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325 make install >>INSTALL.log 2>&1
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326 echo "ok"
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327 cd $cwd
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328 rm -rf $wd/*
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329 rmdir $wd
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330 . ${CONDA_BIN}/deactivate
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331 }
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332 setup_pipeline_environment()
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333 {
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334 echo "+++++++++++++++++++++++++++++++"
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335 echo "Setting up pipeline environment"
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336 echo "+++++++++++++++++++++++++++++++"
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337 # vsearch113
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338 echo -n "Setting up vsearch113..."
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339 if [ -e ${BIN_DIR}/vsearch113 ] ; then
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340 echo "already exists"
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341 elif [ ! -e ${ENV_DIR}/bin/vsearch ] ; then
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342 echo "failed"
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343 fail "vsearch not found"
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344 else
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345 ln -s ${ENV_DIR}/bin/vsearch ${BIN_DIR}/vsearch113
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346 echo "ok"
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347 fi
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348 # fasta_splitter.pl
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349 echo -n "Setting up fasta_splitter.pl..."
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350 if [ -e ${BIN_DIR}/fasta-splitter.pl ] ; then
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351 echo "already exists"
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352 elif [ ! -e ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ] ; then
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353 echo "failed"
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354 fail "fasta-splitter.pl not found"
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355 else
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356 ln -s ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ${BIN_DIR}/fasta-splitter.pl
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357 echo "ok"
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358 fi
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359 # rdp_classifier.jar
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360 local rdp_classifier_jar=rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
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361 echo -n "Setting up rdp_classifier.jar..."
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362 if [ -e ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} ] ; then
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363 echo "already exists"
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364 elif [ ! -e ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ] ; then
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365 echo "failed"
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366 fail "rdp_classifier.jar not found"
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367 else
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368 mkdir -p ${TOP_DIR}/share/rdp_classifier
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369 ln -s ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar}
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370 echo "ok"
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371 fi
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372 # qiime_config
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373 echo -n "Setting up qiime_config..."
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374 if [ -e ${TOP_DIR}/qiime/qiime_config ] ; then
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375 echo "already exists"
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376 else
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377 mkdir -p ${TOP_DIR}/qiime
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378 cat >${TOP_DIR}/qiime/qiime_config <<EOF-qiime-config
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379 qiime_scripts_dir ${ENV_DIR}/bin
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380 EOF-qiime-config
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381 echo "ok"
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382 fi
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383 }
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384 #
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385 # Remove the compilers from the conda environment
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386 # Not sure if this step is necessary
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387 remove_conda_compilers()
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388 {
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389 echo "+++++++++++++++++++++++++++++++++++++++++"
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390 echo "Removing compilers from conda environment"
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391 echo "+++++++++++++++++++++++++++++++++++++++++"
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392 ${CONDA} remove -y -n ${ENV_NAME} gcc_linux-64 gxx_linux-64 gfortran_linux-64
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393 }
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394 #
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|
|
395 # Top level script does the installation
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|
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396 echo "======================================="
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397 echo "Amplicon_analysis_pipeline installation"
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398 echo "======================================="
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399 echo "Installing into ${TOP_DIR}"
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400 if [ -e ${TOP_DIR} ] ; then
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401 fail "Directory already exists"
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402 fi
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403 mkdir -p ${TOP_DIR}
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404 install_conda
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405 install_conda_packages
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406 install_non_conda_packages
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407 setup_pipeline_environment
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408 remove_conda_compilers
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409 echo "===================================="
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410 echo "Amplicon_analysis_pipeline installed"
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411 echo "===================================="
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412 echo ""
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413 echo "Install reference data using:"
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414 echo ""
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415 echo "\$ ${BIN_DIR}/install_reference_data.sh DIR"
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416 echo ""
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417 echo "Run pipeline scripts using:"
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418 echo ""
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419 echo "\$ ${BIN_DIR}/Amplicon_analysis_pipeline.sh ..."
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420 echo ""
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421 echo "(or add ${BIN_DIR} to your PATH)"
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422 echo ""
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423 echo "$(basename $0): finished"
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424 ##
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425 #
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