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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 $1
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26 fi
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27 # Versions
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28 PIPELINE_VERSION=1.3.5
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29 CONDA_REQUIRED_VERSION=4.6.14
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30 RDP_CLASSIFIER_VERSION=2.2
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31 # Directories
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32 TOP_DIR=$(pwd)/Amplicon_analysis-${PIPELINE_VERSION}
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33 BIN_DIR=${TOP_DIR}/bin
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34 CONDA_DIR=${TOP_DIR}/conda
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35 CONDA_BIN=${CONDA_DIR}/bin
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36 CONDA_LIB=${CONDA_DIR}/lib
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37 CONDA=${CONDA_BIN}/conda
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38 ENV_NAME="amplicon_analysis_pipeline@${PIPELINE_VERSION}"
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39 ENV_DIR=${CONDA_DIR}/envs/$ENV_NAME
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40 #
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41 # Functions
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42 #
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43 # Report failure and terminate script
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44 fail()
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45 {
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46 echo ""
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47 echo ERROR $@ >&2
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48 echo ""
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49 echo "$(basename $0): installation failed"
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50 exit 1
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51 }
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52 #
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53 # Rewrite the shebangs in the installed conda scripts
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54 # to remove the full path to conda 'bin' directory
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55 rewrite_conda_shebangs()
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56 {
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57 pattern="s,^#!${CONDA_BIN}/,#!/usr/bin/env ,g"
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58 find ${CONDA_BIN} -type f -exec sed -i "$pattern" {} \;
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59 }
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60 #
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61 # Reset conda version if required
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62 reset_conda_version()
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63 {
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64 CONDA_VERSION="$(${CONDA_BIN}/conda -V 2>&1 | head -n 1 | cut -d' ' -f2)"
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65 echo conda version: ${CONDA_VERSION}
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66 if [ "${CONDA_VERSION}" != "${CONDA_REQUIRED_VERSION}" ] ; then
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67 echo "Resetting conda to last known working version $CONDA_REQUIRED_VERSION"
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68 ${CONDA_BIN}/conda config --set allow_conda_downgrades true
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69 ${CONDA_BIN}/conda install -y conda=${CONDA_REQUIRED_VERSION}
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70 else
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71 echo "conda version ok"
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72 fi
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73 }
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74 #
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75 # Install conda
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76 install_conda()
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77 {
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78 echo "++++++++++++++++"
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79 echo "Installing conda"
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80 echo "++++++++++++++++"
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81 if [ -e ${CONDA_DIR} ] ; then
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82 echo "*** $CONDA_DIR already exists ***" >&2
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83 return
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84 fi
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85 local cwd=$(pwd)
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86 local wd=$(mktemp -d)
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87 cd $wd
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88 wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
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89 bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
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90 echo Installed conda in ${CONDA_DIR}
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91 # Reset the conda version to a known working version
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92 # (to avoid problems observed with e.g. conda 4.7.10)
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93 echo ""
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94 reset_conda_version
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95 # Update the installation files
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96 # This is to avoid problems when the length the installation
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97 # directory path exceeds the limit for the shebang statement
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98 # in the conda files
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99 echo ""
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100 echo -n "Rewriting conda shebangs..."
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101 rewrite_conda_shebangs
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102 echo "ok"
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103 echo -n "Adding conda bin to PATH..."
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104 PATH=${CONDA_BIN}:$PATH
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105 echo "ok"
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106 cd $cwd
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107 rm -rf $wd/*
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108 rmdir $wd
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109 }
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110 #
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111 # Create conda environment
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112 install_conda_packages()
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113 {
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114 echo "+++++++++++++++++++++++++"
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115 echo "Installing conda packages"
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116 echo "+++++++++++++++++++++++++"
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117 local cwd=$(pwd)
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118 local wd=$(mktemp -d)
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119 cd $wd
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120 cat >environment.yml <<EOF
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121 name: ${ENV_NAME}
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122 channels:
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123 - defaults
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124 - conda-forge
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125 - bioconda
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126 dependencies:
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127 - python=2.7
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128 - cutadapt=1.8
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129 - sickle-trim=1.33
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130 - bioawk=1.0
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131 - pandaseq=2.8.1
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132 - spades=3.10.1
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133 - fastqc=0.11.3
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134 - qiime=1.9.1
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135 - blast-legacy=2.2.26
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136 - fasta-splitter=0.2.6
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137 - rdp_classifier=$RDP_CLASSIFIER_VERSION
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138 - vsearch=2.10.4
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139 - r=3.5.1
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140 - r-tidyverse=1.2.1
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141 - bioconductor-dada2=1.8
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142 - bioconductor-biomformat=1.8.0
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143 EOF
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144 ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
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145 echo Created conda environment in ${ENV_DIR}
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146 cd $cwd
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147 rm -rf $wd/*
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148 rmdir $wd
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149 #
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150 # Patch qiime 1.9.1 tools to switch deprecated 'axisbg'
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151 # matplotlib property to 'facecolor':
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152 # https://matplotlib.org/api/prev_api_changes/api_changes_2.0.0.html
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153 echo ""
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154 for exe in make_2d_plots.py plot_taxa_summary.py ; do
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155 echo -n "Patching ${exe}..."
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156 find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/axisbg=/facecolor=/g' {} \;
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157 echo "done"
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158 done
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159 #
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160 # Patch qiime 1.9.1 tools to switch deprecated 'set_axis_bgcolor'
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161 # method call to 'set_facecolor':
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162 # https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.set_axis_bgcolor.html
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163 for exe in make_rarefaction_plots.py ; do
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164 echo -n "Patching ${exe}..."
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165 find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/set_axis_bgcolor/set_facecolor/g' {} \;
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166 echo "done"
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167 done
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168 }
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169 #
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170 # Install all the non-conda dependencies in a single
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171 # function (invokes separate functions for each package)
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172 install_non_conda_packages()
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173 {
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174 echo "+++++++++++++++++++++++++++++"
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175 echo "Installing non-conda packages"
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176 echo "+++++++++++++++++++++++++++++"
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177 # Temporary working directory
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178 local wd=$(mktemp -d)
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179 local cwd=$(pwd)
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180 local wd=$(mktemp -d)
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181 cd $wd
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182 # Amplicon analysis pipeline
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183 echo -n "Installing Amplicon_analysis_pipeline..."
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184 if [ -e ${BIN_DIR}/Amplicon_analysis_pipeline.sh ] ; then
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185 echo "already installed"
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186 else
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187 install_amplicon_analysis_pipeline
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188 echo "ok"
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189 fi
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190 # ChimeraSlayer
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191 echo -n "Installing ChimeraSlayer..."
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192 if [ -e ${BIN_DIR}/ChimeraSlayer.pl ] ; then
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193 echo "already installed"
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194 else
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195 install_chimeraslayer
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196 echo "ok"
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197 fi
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198 # Uclust
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199 # This no longer seems to be available for download from
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200 # drive5.com so don't download
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201 echo "WARNING uclust not available: skipping installation"
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202 }
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203 #
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204 # Amplicon analyis pipeline
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205 install_amplicon_analysis_pipeline()
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206 {
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207 local wd=$(mktemp -d)
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208 local cwd=$(pwd)
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209 local wd=$(mktemp -d)
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210 cd $wd
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211 wget -q https://github.com/MTutino/Amplicon_analysis/archive/${PIPELINE_VERSION}.tar.gz
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212 tar zxf ${PIPELINE_VERSION}.tar.gz
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213 cd Amplicon_analysis-${PIPELINE_VERSION}
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214 INSTALL_DIR=${TOP_DIR}/share/amplicon_analysis_pipeline-${PIPELINE_VERSION}
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215 mkdir -p $INSTALL_DIR
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216 ln -s $INSTALL_DIR ${TOP_DIR}/share/amplicon_analysis_pipeline
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217 for f in *.sh *.R ; do
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218 /bin/cp $f $INSTALL_DIR
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219 done
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220 /bin/cp -r uc2otutab $INSTALL_DIR
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221 mkdir -p ${BIN_DIR}
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222 cat >${BIN_DIR}/Amplicon_analysis_pipeline.sh <<EOF
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223 #!/usr/bin/env bash
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224 #
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225 # Point to Qiime config
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226 export QIIME_CONFIG_FP=${TOP_DIR}/qiime/qiime_config
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227 # Set up the RDP jar file
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228 export RDP_JAR_PATH=${TOP_DIR}/share/rdp_classifier/rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
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229 # Set the Matplotlib backend
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230 export MPLBACKEND="agg"
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231 # Put the scripts onto the PATH
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232 export PATH=${BIN_DIR}:${INSTALL_DIR}:\$PATH
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233 # Activate the conda environment
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234 export PATH=${CONDA_BIN}:\$PATH
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235 source ${CONDA_BIN}/activate ${ENV_NAME}
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236 # Execute the driver script with the supplied arguments
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237 $INSTALL_DIR/Amplicon_analysis_pipeline.sh \$@
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238 exit \$?
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239 EOF
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240 chmod 0755 ${BIN_DIR}/Amplicon_analysis_pipeline.sh
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241 cat >${BIN_DIR}/install_reference_data.sh <<EOF
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242 #!/usr/bin/env bash -e
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243 #
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244 function usage() {
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245 echo "Usage: \$(basename \$0) DIR"
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246 }
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247 if [ -z "\$1" ] ; then
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248 usage
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249 exit 0
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250 elif [ "\$1" == "--help" ] || [ "\$1" == "-h" ] ; then
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251 usage
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252 echo ""
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253 echo "Install reference data into DIR"
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254 exit 0
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255 fi
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256 echo "=========================================="
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257 echo "Installing Amplicon analysis pipeline data"
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258 echo "=========================================="
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259 if [ ! -e "\$1" ] ; then
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260 echo "Making directory \$1"
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261 mkdir -p \$1
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262 fi
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263 cd \$1
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264 DATA_DIR=\$(pwd)
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265 echo "Installing reference data under \$DATA_DIR"
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266 $INSTALL_DIR/References.sh
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267 echo ""
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268 echo "Use '-r \$DATA_DIR' when running Amplicon_analysis_pipeline.sh"
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269 echo "to use the reference data from this directory"
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270 echo ""
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271 echo "\$(basename \$0): finished"
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272 EOF
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273 chmod 0755 ${BIN_DIR}/install_reference_data.sh
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274 cd $cwd
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275 rm -rf $wd/*
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276 rmdir $wd
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277 }
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278 #
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279 # ChimeraSlayer
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280 install_chimeraslayer()
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281 {
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282 local cwd=$(pwd)
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283 local wd=$(mktemp -d)
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284 cd $wd
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285 wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
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286 tar zxf microbiomeutil_2010-04-29.tar.gz
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287 cd microbiomeutil_2010-04-29
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288 INSTALL_DIR=${TOP_DIR}/share/microbiome_chimeraslayer-2010-04-29
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289 mkdir -p $INSTALL_DIR
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290 ln -s $INSTALL_DIR ${TOP_DIR}/share/microbiome_chimeraslayer
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291 /bin/cp -r ChimeraSlayer $INSTALL_DIR
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292 cat >${BIN_DIR}/ChimeraSlayer.pl <<EOF
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293 #!/usr/bin/env bash
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294 export PATH=$INSTALL_DIR:\$PATH
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295 $INSTALL_DIR/ChimeraSlayer/ChimeraSlayer.pl $@
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296 EOF
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297 chmod 0755 ${INSTALL_DIR}/ChimeraSlayer/ChimeraSlayer.pl
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298 chmod 0755 ${BIN_DIR}/ChimeraSlayer.pl
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299 cd $cwd
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300 rm -rf $wd/*
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301 rmdir $wd
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302 }
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303 #
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304 # uclust required for QIIME/pyNAST
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305 # License only allows this version to be used with those two packages
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306 # See: http://drive5.com/uclust/downloads1_2_22q.html
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307 install_uclust()
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308 {
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309 local cwd=$(pwd)
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310 local wd=$(mktemp -d)
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311 cd $wd
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312 wget -q http://drive5.com/uclust/uclustq1.2.22_i86linux64
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313 INSTALL_DIR=${TOP_DIR}/share/uclust-1.2.22
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314 mkdir -p $INSTALL_DIR
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315 ln -s $INSTALL_DIR ${TOP_DIR}/share/uclust
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316 /bin/mv uclustq1.2.22_i86linux64 ${INSTALL_DIR}/uclust
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317 chmod 0755 ${INSTALL_DIR}/uclust
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318 ln -s ${INSTALL_DIR}/uclust ${BIN_DIR}
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319 cd $cwd
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320 rm -rf $wd/*
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321 rmdir $wd
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322 }
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323 setup_pipeline_environment()
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324 {
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325 echo "+++++++++++++++++++++++++++++++"
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326 echo "Setting up pipeline environment"
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327 echo "+++++++++++++++++++++++++++++++"
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328 # fasta_splitter.pl
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329 echo -n "Setting up fasta_splitter.pl..."
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330 if [ -e ${BIN_DIR}/fasta-splitter.pl ] ; then
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331 echo "already exists"
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332 elif [ ! -e ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ] ; then
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333 echo "failed"
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334 fail "fasta-splitter.pl not found"
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335 else
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336 ln -s ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ${BIN_DIR}/fasta-splitter.pl
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337 echo "ok"
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338 fi
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339 # rdp_classifier.jar
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340 local rdp_classifier_jar=rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
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341 echo -n "Setting up rdp_classifier.jar..."
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342 if [ -e ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} ] ; then
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343 echo "already exists"
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344 elif [ ! -e ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ] ; then
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345 echo "failed"
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346 fail "rdp_classifier.jar not found"
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347 else
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348 mkdir -p ${TOP_DIR}/share/rdp_classifier
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349 ln -s ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar}
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350 echo "ok"
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351 fi
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352 # qiime_config
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353 echo -n "Setting up qiime_config..."
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354 if [ -e ${TOP_DIR}/qiime/qiime_config ] ; then
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355 echo "already exists"
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356 else
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357 mkdir -p ${TOP_DIR}/qiime
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358 cat >${TOP_DIR}/qiime/qiime_config <<EOF-qiime-config
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359 qiime_scripts_dir ${ENV_DIR}/bin
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360 EOF-qiime-config
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361 echo "ok"
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362 fi
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363 }
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364 #
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365 # Top level script does the installation
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366 echo "======================================="
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367 echo "Amplicon_analysis_pipeline installation"
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368 echo "======================================="
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369 echo "Installing into ${TOP_DIR}"
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370 if [ -e ${TOP_DIR} ] ; then
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371 fail "Directory already exists"
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372 fi
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373 mkdir -p ${TOP_DIR}
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374 install_conda
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375 install_conda_packages
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376 install_non_conda_packages
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377 setup_pipeline_environment
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378 echo "===================================="
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379 echo "Amplicon_analysis_pipeline installed"
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380 echo "===================================="
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381 echo ""
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382 echo "Install reference data using:"
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383 echo ""
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384 echo "\$ ${BIN_DIR}/install_reference_data.sh DIR"
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385 echo ""
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386 echo "Run pipeline scripts using:"
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387 echo ""
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388 echo "\$ ${BIN_DIR}/Amplicon_analysis_pipeline.sh ..."
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389 echo ""
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390 echo "(or add ${BIN_DIR} to your PATH)"
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391 echo ""
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392 echo "$(basename $0): finished"
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393 ##
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394 #
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