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1 #!/bin/bash
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2
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3 # Copyleft ↄ⃝ 2012 Institut Curie
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4 # Author(s): Jocelyn Brayet, Laurene Syx, Chongjian Chen, Nicolas Servant(Institut Curie) 2012 - 2015
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5 # Contact: bioinfo.ncproseq@curie.fr
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6 # This software is distributed without any guarantee under the terms of the GNU General
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7 # Public License, either Version 2, June 1991 or Version 3, June 2007.
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8
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9 while getopts "i:s:n:g:m:o:f:r:h:p:l:t:a:q:d:" optionName; do
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10 case "$optionName" in
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11
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12 i) INPUT+="$OPTARG,";;
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13 s) SAMPLENAME+="$OPTARG,";;
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14 n) PROJECTNAME="$OPTARG";;
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15 g) GENOME="$OPTARG";;
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16 m) RMSK="$OPTARG";;
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17 o) BAM_OUT+="$OPTARG,";;
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18 f) RFAM="$OPTARG";;
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19 r) REPORT="$OPTARG";;
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20 h) HTML_REPORT="$OPTARG";;
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21 p) PDF_REPORT="$OPTARG";;
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22 l) LOG_FILE="$OPTARG";;
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23 t) INPUT_TYPE="$OPTARG";;
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24 a) ALIGNMENT="$OPTARG";;
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25 q) FASTQ_FORMAT+="$OPTARG,";;
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26 d) ROOT_DIR="$OPTARG";;
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27
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28 esac
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29 done
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30
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31 ##### ncPRO-seq annotation - Galaxy #####
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32
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33 GENOME_2=`echo $GENOME | cut -d"_" -f2`
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34
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35 databasePath=$ROOT_DIR/database/files
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36
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37 mkdir -p $databasePath/ncproseqAnnotation
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38 mkdir -p $databasePath/ncproseqAnnotation/annotation
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39 annotationPath=$databasePath/ncproseqAnnotation/annotation
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40 [ ! -d $annotationPath/$GENOME_2 ] && wget http://ncpro.curie.fr/ncproseq/install_dir/annotation/$GENOME.tar.gz -P $annotationPath -q && cd $annotationPath && tar -zxf $GENOME.tar.gz && rm -rf $GENOME.tar.gz
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41
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42 #########
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43
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44
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45 sampleArray=(${INPUT//,/ })
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46 nameArray=(${SAMPLENAME//,/ })
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47 bamArray=(${BAM_OUT//,/ })
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48
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49 if [[ $REPORT == "pdf" ]];then
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50 OUTPUT_PATH_DIR=`dirname $LOG_FILE`
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51 OUTPUT_PATH_NAME=`basename $LOG_FILE .dat`
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52 else
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53 OUTPUT_PATH_DIR=`dirname $HTML_REPORT`
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54 OUTPUT_PATH_NAME=`basename $HTML_REPORT .dat`
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55 fi
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56
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57 OUTPUT_PATH="${OUTPUT_PATH_DIR}/${OUTPUT_PATH_NAME}_files"
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58
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59
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60
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61 #ME
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62 mkdir -p $OUTPUT_PATH
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63
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64 chmod 777 -R $OUTPUT_PATH
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65
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66 #VERSION=`echo $OUTPUT_PATH | cut -d"/" -f3`
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67 #VERSION=`echo $VERSION | cut -d"_" -f2`
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68
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69 #DEBUG_MODE
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70
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71 DEBUG_MODE="on"
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72 DEBUG="/dev/null"
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73
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74 if [[ $DEBUG_MODE == "on" ]];then
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75
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76 DEBUG="$OUTPUT_PATH/ncPRO-QC.debug"
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77
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78 fi
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79
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80 #Deploy ncPRO directories structure
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81
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82 /usr/curie_ngs/ncproseq_v1.6.5/bin/ncPRO-deploy -o $OUTPUT_PATH > $DEBUG
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83
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84 echo "$INPUT" >> $DEBUG
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85 echo "$SAMPLENAME" >> $DEBUG
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86 echo "$PROJECTNAME" >> $DEBUG
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87 echo "$GENOME_2" >> $DEBUG
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88 echo "$RMSK" >> $DEBUG
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89 echo "$BAM_OUT" >> $DEBUG
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90 echo "$RFAM" >> $DEBUG
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91 echo "$REPORT" >> $DEBUG
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92 echo "$HTML_REPORT" >> $DEBUG
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93 echo "$PDF_REPORT" >> $DEBUG
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94 echo "$LOG_FILE" >> $DEBUG
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95 echo "$INPUT_TYPE" >> $DEBUG
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96 echo "$ALIGNMENT" >> $DEBUG
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97
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98 echo "$sampleArray" >> $DEBUG
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99 echo "$nameArray" >> $DEBUG
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100 echo "$bamArray" >> $DEBUG
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101
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102 #Go to working directory
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103
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104 cp -rf /usr/curie_ngs/ncproseq_v1.6.5/annotation/*.item $annotationPath
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105 cp -rf /usr/curie_ngs/ncproseq_v1.6.5/annotation/*_items.txt $annotationPath
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106
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107 if [[ ! -L "$databasePath/ncproseqBowtieIndexes" && ! -d "$databasePath/ncproseqBowtieIndexes" ]]
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108 then
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109 mkdir -p $databasePath/ncproseqBowtieIndexes
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110 fi
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111
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112 cd /usr/curie_ngs
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113 rm -rf bowtie_indexes
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114 ln -s $databasePath/ncproseqBowtieIndexes bowtie_indexes
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115
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116 cd $OUTPUT_PATH
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117
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118 rm annotation
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119
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120 ln -s $annotationPath annotation
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121
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122 rm manuals
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123
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124 #Create symbolic link to input
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125 #********************************************************************************* NEW: for BAM files, check if reads in input are grouped or not and change cmd accordignly ***********
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126 if [[ $INPUT_TYPE == "fastq" ]];then
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127
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128 count=0
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129 for i in ${sampleArray[*]}
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130 do
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131 ln -s $i ${OUTPUT_PATH}/rawdata/${nameArray[count]}.fastq
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132 count=$(( $count + 1 ))
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133 done
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134 fi
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135
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136 if [[ $INPUT_TYPE == "bam" ]];then
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137
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138 count=0
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139 for i in ${sampleArray[*]}
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140 do
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141 ln -s $i ${OUTPUT_PATH}/rawdata/${nameArray[count]}.bam
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142 count=$(( $count + 1 ))
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143
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144 #check if grouped
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145 RG=`samtools view $i | awk --posix 'BEGIN {RG=1} { if ($1 !~ /^[0-9]{1,}_[0-9]{1,}$/) {RG=0 ; exit} } END { print RG}'`
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146 done
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147 fi
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148
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149 #Edit config-ncrna.txt ##### A REFAIRE ####
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150 CONFIG_FILE=config-ncrna.txt
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151
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152 sed -i "s:^BOWTIE_GENOME_REFERENCE =.*$:BOWTIE_GENOME_REFERENCE = $GENOME_2:g" $CONFIG_FILE
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153 sed -i "s:^ORGANISM.*$:ORGANISM = $GENOME_2:g" $CONFIG_FILE
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154
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155 sed -i "/N_CPU/c\N_CPU = 6" $CONFIG_FILE #****** Make sure this value matches universe.ini files
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156 sed -i "s/test_Curie/$PROJECTNAME/g" $CONFIG_FILE
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157 sed -i "s:^FASTQ_FORMAT =.*$:FASTQ_FORMAT = $FASTQ_FORMAT:g" $CONFIG_FILE
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158
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159
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160 if [[ -f "$annotationPath/$GENOME_2/cluster_pirna.gff" ]]
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161 then
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162 ANNO_CATALOG="$annotationPath/$GENOME_2/precursor_miRNA.gff $annotationPath/$GENOME_2/rfam.gff $annotationPath/$GENOME_2/cluster_pirna.gff $annotationPath/$GENOME_2/rmsk.gff $annotationPath/$GENOME_2/coding_gene.gff"
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163 else
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164 if [[ -f "$annotationPath/$GENOME_2/pirna.gff" ]]
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165 then
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166 ANNO_CATALOG="$annotationPath/$GENOME_2/precursor_miRNA.gff $annotationPath/$GENOME_2/rfam.gff $annotationPath/$GENOME_2/pirna.gff $annotationPath/$GENOME_2/rmsk.gff $annotationPath/$GENOME_2/coding_gene.gff"
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167 else
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168 ANNO_CATALOG="$annotationPath/$GENOME_2/precursor_miRNA.gff $annotationPath/$GENOME_2/rfam.gff $annotationPath/$GENOME_2/rmsk.gff $annotationPath/$GENOME_2/coding_gene.gff"
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169 fi
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170 fi
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171
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172 sed -i "s:^ANNO_CATALOG.*$:ANNO_CATALOG = $ANNO_CATALOG:g" $CONFIG_FILE
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173
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174 #Build command line
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175
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176 if [[ $INPUT_TYPE == "fastq" ]];then
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177
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178 if [[ $ALIGNMENT == "True" ]]; then
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179
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180
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181 COMMAND_LINE="-c $CONFIG_FILE -s processRead -s mapGenome -s mapGenomeStat -s mapAnnOverview"
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182
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183 if [[ $RFAM == "True" ]];then
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184
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185 COMMAND_LINE="$COMMAND_LINE -s overviewRfam -s overviewRmsk"
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186
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187 fi
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188
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189 else
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190
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191 COMMAND_LINE="-c $CONFIG_FILE -s processRead"
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192
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193 fi
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194
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195 fi
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196
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197
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198
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199 #### NEW if BAM already grouped, omit [ -s processBam ] + put input.bam in /bowtie_results
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200 if [[ $INPUT_TYPE == "bam" ]];then
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201
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202 if [[ $RG = 0 ]]; then #if bam file is NOT grouped
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203
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204 COMMAND_LINE="-c $CONFIG_FILE -s processBam -s mapGenomeStat -s mapAnnOverview"
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205
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206 else
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207
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208 count=0
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209 for i in ${sampleArray[*]}
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210 do
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211 ln -s $i ${OUTPUT_PATH}/rawdata/${nameArray[count]}.bam
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212 count=$(( $count + 1 ))
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213 done
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214 COMMAND_LINE="-c $CONFIG_FILE -s mapGenomeStat -s mapAnnOverview"
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215 fi
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216
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217
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218 if [[ $RFAM == "True" ]];then
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219
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220 COMMAND_LINE="$COMMAND_LINE -s overviewRfam -s overviewRmsk"
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221
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222 fi
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223
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224 fi
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225
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226 #************************* new
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227
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228 ##### Function to create HTML report in Galaxy ######
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229
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230 function createHtmlReport
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231 {
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232
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233 # galaxy part :
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234
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235 #Reformat html output
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236
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237 tr '>' '\n' < ${OUTPUT_PATH}/report.html | sed -ne "s@.*<img src='\([^']*\)'.*@\1@p" -e 's@.*<img src="\([^"]*\)".*@\1@p' > ${OUTPUT_PATH}/img_list.txt
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238
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239 NC_LOGO=`head -1 ${OUTPUT_PATH}/img_list.txt`
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240
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241 #HTTP_PATH=`echo $OUTPUT_PATH | sed "s/\/data\/kdi_${VERSION}/http:\/\/data-kdi-${VERSION}.curie.fr\/file/g"`
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242
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243 i=1
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244
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245 if [[ $INPUT_TYPE == "fastq" ]];then
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246
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247 echo "<p align=center><img src=$NC_LOGO></p><p align=center><b><u>QUALITY CONTROL</u></b></p>" > ${HTML_REPORT}
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248 fi
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249
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250 if [[ $INPUT_TYPE == "bam" ]];then
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251
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252 echo "<p align=center><img src=$NC_LOGO></p><p align=center><b><u>DATA MAPPING</u></b></p>" > $HTML_REPORT
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253 fi
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254
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255 while read line
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256 do
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257
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258 if [[ $line != "" ]];then
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259
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260 if [[ $i == "3" ]];then
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261
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262 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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263
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264 if [[ $INPUT_TYPE == "fastq" ]];then
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265 echo "<p align=center><b>Base Composition Information</b></p><table align=center><tr><td align=center><a href=$ahref><img src=$line></a></td>" >> $HTML_REPORT
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266 fi
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267
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268 if [[ $INPUT_TYPE == "bam" ]];then
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269 echo "<p align=center><b>Mapping proportions</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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270 fi
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271
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272 fi
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273
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274 if [[ $i == "4" ]];then
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275
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276 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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277
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278 if [[ $INPUT_TYPE == "fastq" ]];then
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279 echo "<td align=center><a href=$ahref><img src=$line></td></a></td><table>" >> $HTML_REPORT
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280 fi
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281
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282 if [[ $INPUT_TYPE == "bam" ]];then
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283 echo "<hr width=500><p align=center><b>Distinct Reads Length Distribution</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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284 fi
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285
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286 fi
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287
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288 if [[ $i == "5" ]];then
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289
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290 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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291
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292 if [[ $INPUT_TYPE == "fastq" ]];then
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293 echo "<hr width=500><p align=center><b>Distinct Reads Length Distribution</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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294 fi
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295
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296 if [[ $INPUT_TYPE == "bam" ]];then
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297 echo "<hr width=500><p align=center><b>Abundant Reads Length Distribution</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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298 fi
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299
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300 fi
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301
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302 if [[ $i == "6" ]];then
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303
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304 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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305
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306 if [[ $INPUT_TYPE == "fastq" ]];then
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307 echo "<hr width=500><p align=center><b>Quality Score</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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308 fi
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309
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310 if [[ $INPUT_TYPE == "bam" ]];then
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311 echo "<hr size=20><p align=center style=font-size:25px;><b><u>ncRNAs OVERVIEW</u></b><p align=center><b>Reads Annotation Overview</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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312 fi
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313
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314 fi
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315
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316 if [[ $i == "7" ]];then
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317
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318 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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319 if [[ $INPUT_TYPE == "fastq" ]];then
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320 echo "<hr width=500><p align=center><b>Abundant Reads Length Distribution</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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321 fi
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322 if [[ $INPUT_TYPE == "bam" ]];then
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323
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324 if [[ $RFAM == "True" ]];then
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325 echo "<p align=center><b>Precursor miRNAs Annotation</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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326 else
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327 break
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328 fi
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329 fi
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330 fi
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331
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332 if [[ $i == "8" ]];then
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333
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334 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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335 if [[ $INPUT_TYPE == "fastq" ]];then
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336
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337 if [[ $ALIGNMENT == "True" ]]; then
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338
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339 echo "<hr size=20><p align=center style=font-size:25px;><b><u>DATA MAPPING</u></b></p><p align=center><b>Mapping proportions</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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340 else
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341 break
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342 fi
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343 fi
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344 if [[ $INPUT_TYPE == "bam" ]];then
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345
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346 echo "<p align=center><b>Annotation of ncRNAs from RFAM</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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347 fi
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348 fi
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349
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350 if [[ $i == "9" ]];then
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351
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352 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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353 if [[ $INPUT_TYPE == "fastq" ]];then
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354 echo "<hr width=500><p align=center><b>Distinct Reads Length Distribution</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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355 fi
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356
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357 if [[ $INPUT_TYPE == "bam" ]];then
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358
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359 echo "<p align=center><b>Annotation of Repetitive Regions</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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360 break
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361 fi
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362
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363 fi
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364
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365 if [[ $i == "10" ]];then
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366
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367 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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368
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369 echo "<hr width=500><p align=center><b>Abundant Reads Length Distribution</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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370
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371 fi
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372
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373 if [[ $i == "11" ]];then
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374
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375 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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376
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377 echo "<hr size=20><p align=center style=font-size:25px;><b><u>ncRNAs OVERVIEW</u></b><p align=center><b>Reads Annotation Overview</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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378
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379 fi
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380
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381 if [[ $RFAM == "True" ]];then
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382
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383 if [[ $i == "12" ]];then
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384
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385 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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386
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387 echo "<p align=center><b>Precursor miRNAs Annotation</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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388
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389 fi
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390
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391 if [[ $i == "13" ]];then
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392
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393 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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394
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395 echo "<p align=center><b>Annotation of ncRNAs from RFAM</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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396
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397 fi
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398
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399 if [[ $i == "14" ]];then
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400
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401 ahref=`sed "s/html\/thumb/pic/" <<< $line`
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402
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403 echo "<p align=center><b>Annotation of Repetitive Regions</b></p><p align=center><a href=$ahref><img src=$line></a></p>" >> $HTML_REPORT
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|
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404
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405 fi
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406
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407 fi
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408
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|
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409 i=$(( $i + 1 ))
|
|
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410
|
|
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411 fi
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|
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412
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413
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414 done < ${OUTPUT_PATH}/img_list.txt
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415
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416 rm ${OUTPUT_PATH}/img_list.txt
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417
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418
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|
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419
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|
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420 }
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421
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422
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423 #Launch ncPRO analysis
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424
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|
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425 #FAIRE une boucle pour -s hrml_builder ou -s pdf_builder
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426
|
|
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427 if [[ $REPORT == "all" ]];then
|
|
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428
|
|
|
429
|
|
|
430 /usr/curie_ngs/ncproseq_v1.6.5/bin/ncPRO-seq $COMMAND_LINE -s html_builder -s pdf_builder>> $DEBUG
|
|
|
431
|
|
|
432 createHtmlReport
|
|
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433
|
|
|
434 cp ${OUTPUT_PATH}/Analysis_report_ncPRO-seq.pdf $PDF_REPORT
|
|
|
435
|
|
|
436 fi
|
|
|
437
|
|
|
438 if [[ $REPORT == "pdf" ]];then
|
|
|
439
|
|
|
440
|
|
|
441 /usr/curie_ngs/ncproseq_v1.6.5/bin/ncPRO-seq $COMMAND_LINE -s pdf_builder>> $DEBUG
|
|
|
442
|
|
|
443 cp ${OUTPUT_PATH}/Analysis_report_ncPRO-seq.pdf $PDF_REPORT
|
|
|
444
|
|
|
445
|
|
|
446 fi
|
|
|
447
|
|
|
448 if [[ $REPORT == "html" ]];then
|
|
|
449
|
|
|
450
|
|
|
451 /usr/curie_ngs/ncproseq_v1.6.5/bin/ncPRO-seq $COMMAND_LINE -s html_builder>> $DEBUG
|
|
|
452
|
|
|
453 createHtmlReport
|
|
|
454
|
|
|
455 fi
|
|
|
456
|
|
|
457 #Galaxy output handling
|
|
|
458
|
|
|
459 cp ${OUTPUT_PATH}/pipeline.log $LOG_FILE
|
|
|
460
|
|
|
461 if [[ $ALIGNMENT == "True" ]];then
|
|
|
462
|
|
|
463 count=0
|
|
|
464 for i in ${bamArray[*]}
|
|
|
465 do
|
|
|
466 cp ${OUTPUT_PATH}/bowtie_results/${nameArray[count]/_/.}_$GENOME_2.bam $i
|
|
|
467 count=$(( $count + 1 ))
|
|
|
468 done
|
|
|
469 fi
|
