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annotate beast.sh @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 #!/bin/bash
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2
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3 source $(dirname $0)/util.sh
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4 source $1
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5
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6
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7 # COMPUTE METADATA IF NEEDED!
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8 # ===========================
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9
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10 if [[ $METADATA_SPECIFICATION == "regex" ]]
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11 then
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12 # First make sure we actually have an alignment to operate on
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13 if [[ ${ALIGNMENT} == "" ]]
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14 then
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15 echo "Must have alignment in order to specify metadata via regular expression" > /dev/stderr
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16 exit 1
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17 fi
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18 DEME_COLUMN="deme"
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19 # If we have a regex, will need to create the specification file to pass along
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20 if [[ $DATE_REGEX != "" ]]
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21 then
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22 DATE_REGEX_FLAG="-t $DATE_REGEX"
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23 # Need to let things know downstream that there is a date column in the constructed metadata
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24 DATE_COLUMN="date"
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25 else
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26 DATE_REGEX_FLAG=""
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27 DATE_COLUMN=""
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28 fi
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29 metadata_from_seqnames.py -d "$DEME_REGEX" ${DATE_REGEX_FLAG} \
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30 ${ALIGNMENT} tmp_deme_spec.csv
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31 METADATA_FILE=tmp_deme_spec.csv
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32 fi
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33
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34
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35
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36 # HANDLE DOWNSAMPLING
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37 # ===================
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38
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39 if [[ $DOWNSAMPLING_METHOD != "none" ]]
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40 then
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41 if [[ $METADATA_FILE == "" || $ALIGNMENT == "" ]]
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42 then
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43 echo "Must specify deme and alignment data in order to downsample" > /dev/stdout
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44 exit 1
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45 fi
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46 if [[ $DOWNSAMPLING_RANDOM_SEED == "" ]]
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47 then
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48 DOWNSAMPLING_RANDOM_SEED=$RANDOM
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49 echo "You did not specify a random seed for this run, so this one is being used, in case you'd like to
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50 reproduce your results: $DOWNSAMPLING_RANDOM_SEED"
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51 else
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52 DS_RANDOM_SEED_FLAG="-s $DOWNSAMPLING_RANDOM_SEED"
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53 fi
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54 # This script does the downsampling
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55 deme_downsample.py $DS_RANDOM_SEED_FLAG -m $DOWNSAMPLING_METHOD -k $DOWNSAMPLING_K -c $DEME_COLUMN \
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56 $ALIGNMENT $METADATA_FILE \
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57 $DOWNSAMPLED_ALIGNMENT downsampled_metadata.csv
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58 # Assign these to the unsampled variable names so the code below follows the same flow regardless
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59 ALIGNMENT=$DOWNSAMPLED_ALIGNMENT
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60 METADATA_FILE=downsampled_metadata.csv
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61 # If we are downsampling and specified a metadata file, make sure to return a downsampled_metadata file
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62 if [[ $METADATA_SPECIFICATION == "file" ]]
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63 then
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64 cp downsampled_metadata.csv $DOWNSAMPLED_METADATA
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65 fi
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66 fi
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67
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68
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69
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70 # CONSTRUCT BEASTFILE AND RUN BEAST
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71 # =================================
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72
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73 # Make a metadata flag we can pass into the format command
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74 if [[ $METADATA_FILE != "" ]]
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75 then
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76 # Then use either the file given to us, or the one we constructed from regexprs
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77 META_FLAG="-m $METADATA_FILE"
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78 else
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79 META_FLAG=""
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80 fi
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81
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82 # Make a metadata flag we can pass into the format command
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83 if [[ $ALIGNMENT != "" ]]
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84 then
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85 # Then use either the file given to us, or the one we constructed from regexprs
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86 ALIGNMENT_FLAG="-a $ALIGNMENT"
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87 else
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88 ALIGNMENT_FLAG=""
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89 fi
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90
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91 # Set the default BEASTfile
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92 if [ $BEASTFILE_SPECIFICATION == "default" ]
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93 then
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94 # ARGO_TOOL_DIR gets defined in utils; magick sauce...
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95 BEASTFILE_TEMPLATE=$ARGO_TOOL_DIR/default_beastfile_template.xml
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96 fi
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97
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98 # Fork on a bunch of things based on whether this is a resume run or not
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99 if [ $RESUME_SELECTOR == "true" ]
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100 then
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101 # There should be a specified beastfile if we're resuming, otherwise raise
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102 if [ $BEASTFILE_SPECIFICATION == "default" ]
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103 then
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104 echo "Must specify the beastfile output by last run if doing a resume run" > /dev/stdout
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105 exit 1
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106 fi
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107 # Take care of getting things set up for proper formatting and resuming
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108 FORMAT_ARGS="$SAMPLES_FLAG" # We don't want to accept any beastfile modifications except samples
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109 RESUME_FLAG="-resume"
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110 cp $RESUME_LOGFILE posterior.log
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111 cp $RESUME_TREEFILE posterior.trait.trees
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112 # We assure this state location works by renaming the beastfile to beastfile.xml later
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113 cp $RESUME_STATEFILE beastfile.xml.state
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114 else
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115 # Otherwise, set the full flag collection
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116 RESUME_FLAG=""
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117 FORMAT_ARGS="$ALIGNMENT_FLAG $META_FLAG $SAMPLES_FLAG $SAMPLING_INTERVAL_FLAG"
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118 # Add deme information only if we know what column it is (which will only be if we have metadata or regexs)
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119 if [[ $DATE_COLUMN != "" ]]
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120 then
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121 FORMAT_ARGS="$FORMAT_ARGS -d $DEME_COLUMN"
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122 fi
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123 # Add the date information only if a date column is specified
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124 if [[ $DATE_COLUMN != "" ]]
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125 then
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126 FORMAT_ARGS="$FORMAT_ARGS -D $DATE_COLUMN"
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127 fi
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128 fi
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129
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130 # Format our beastfile
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131 format_beastfile.py $BEASTFILE_TEMPLATE $FORMAT_ARGS $FORMATTED_BEASTFILE
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132
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133 # Actually run BEAST and set the output vars to their locations
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134 cp $FORMATTED_BEASTFILE beastfile.xml
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135
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136 # BEAST should be in our path from the argo_env requirement
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137 beast $RANDOM_SEED_FLAG $RESUME_FLAG beastfile.xml
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138
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139 # Copy files over to the locations Galaxy has specified for them
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140 cp posterior.log $LOGFILE
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141 cp posterior.trait.trees $TREEFILE
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142 cp beastfile.xml.state $STATEFILE
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143
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144
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145 # LOGFILE TRIMMING FOR RESUME RUNS
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146 # ================================
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147
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148 if [ $RESUME_SELECTOR == "true" ]
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149 then
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150 posterior-subset -t logfile -c $RESUME_SAMPLES $LOGFILE $TRIMMED_LOGFILE
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151 posterior-subset -t treefile -c $RESUME_SAMPLES $TREEFILE $TRIMMED_TREEFILE
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152 ess.py --html-out $TRIMMED_LOGFILE $ESS
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153 else
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154 ess.py --html-out $LOGFILE $ESS
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155 fi
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156
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157
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158
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159