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author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
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2
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3 The Mothur Tool Suite repository:
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4 - Provides Mothur wrappers for most Mothur tools
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5 - Data type used by mothur and other metagenomics tools
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6 - Downloads and builds Mothur on the Linux or Mac operating system
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7
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8 Requirements:
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9 - Build utilities (make, GCC, gfortran, etc)
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10 - simplejson (pip install simplejson)
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11
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12 Repository Dependency:
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13 - BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)
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14 - The repository name should be package_blast_2_2_26 so it matches with the tool dependency.
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15
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16
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17 Manual installation for Mothur:
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18 Install mothur v.1.33 on your galaxy system so galaxy can execute the mothur command
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19 ( This version of wrappers is designed for Mothur version 1.33- it may work on later versions )
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20 http://www.mothur.org/wiki/Download_mothur
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21 http://www.mothur.org/wiki/Installation
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22 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
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23
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24 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
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25 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
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26 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
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27 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
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28 Install in galaxy: tool-data/shared/jars/TreeVector.jar
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29
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30 Install reference data from silva and greengenes
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31 RDP reference file (modified for mothur):
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32 http://www.mothur.org/wiki/RDP_reference_files
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33 - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
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34 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
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35 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
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36 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
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37 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
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38 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
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39 Silva reference:
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40 http://www.mothur.org/wiki/Silva_reference_files
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41 - Bacterial references (14,956 sequences)
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42 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
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43 - Archaeal references (2,297 sequences)
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44 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
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45 - Eukaryotic references (1,238 sequences)
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46 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
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47 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
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48 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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49 Alignment database rRNA gene sequences:
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50 http://www.mothur.org/wiki/Alignment_database
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51 - greengenes reference alignment
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52 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
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53 - SILVA (Silva reference)
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54 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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55 Secondary structure mapping files:
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56 http://www.mothur.org/wiki/Secondary_structure_map
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57 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
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58 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
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59 Lane masks:
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60 http://www.mothur.org/wiki/Lane_mask
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61 greengenes-compatible mask:
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62 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
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63 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
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64 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
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65 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
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66 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
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67 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
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68 SILVA-compatible mask:
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69 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
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70 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
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71 Lookup Files for sff flow analysis using shhh.flows:
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72 http://www.mothur.org/wiki/Alignment_database
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73
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74 Example from UMN installation: (We also made these available in a Galaxy public data library)
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75 /project/db/galaxy/mothur/Silva.bacteria.zip
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76 /project/db/galaxy/mothur/silva.eukarya.fasta
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77 /project/db/galaxy/mothur/Greengenes.alignment.zip
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78 /project/db/galaxy/mothur/Silva.archaea.zip
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79 /project/db/galaxy/mothur/Silva_ss_map.zip
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80 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
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81 /project/db/galaxy/mothur/Silva.gold.bacteria.zip
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82 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
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83 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
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84 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
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85 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
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86 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
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87 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
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88 /project/db/galaxy/mothur/nogap.eukarya.fasta
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89 /project/db/galaxy/mothur/silva.eukarya.silva.tax
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90 /project/db/galaxy/mothur/silva.gold.align
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91 /project/db/galaxy/mothur/silva.ss.map
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92 /project/db/galaxy/mothur/gg.ss.map
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93 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
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94 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
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95 /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
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96 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
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97 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
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98 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
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99 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
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100 /project/db/galaxy/mothur/Silva.eukarya.zip
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101 /project/db/galaxy/mothur/Gg_ss_map.zip
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102 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
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103 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
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104 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
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105 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
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106 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
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107 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
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108 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
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109 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
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110 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
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111
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112 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
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113 tool-data/mothur_aligndb.loc
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114 tool-data/mothur_map.loc
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115 tool-data/mothur_taxonomy.loc
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116 tool-data/shared/jars/TreeVector.jar
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117
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118 ################################################################
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119 #### If you are manually adding this to your local galaxy: ####
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120 ################################################################
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121
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122 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
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123
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124 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
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125
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126 add the following import line to: lib/galaxy/datatypes/registry.py
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127 import metagenomics # added for metagenomics mothur
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128
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129 add datatypes to: datatypes_conf.xml
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130
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131 add mothur tools to: tool_conf.xml
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132
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133 ############ DESIGN NOTES #########################################################################################################
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134 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
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135
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136 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
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137
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138 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
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139 * Every tool will produce the logfile of the mothur run as an output.
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140 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
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141 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
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142 are included in the --new_datasets parameter to mothur_wrapper.py
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143
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144 Here is an example call to the mothur_wrapper.py script with an explanation before each param :
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145 mothur_wrapper.py
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146 # name of a mothur command, this is required
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147 --cmd='summary.shared'
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148 # Galaxy output dataset list, these are output files that can be determined before the command is run
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149 # The items in the list are separated by commas
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150 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
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151 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
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152 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
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153 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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154 # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation (when number of outputs not known in advance)
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155 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
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156 --datasetid='2578'
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157 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
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158 --new_file_path='$__new_file_path__'
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159 # specifies files to copy to the new_file_path
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160 # The list is separated by commas
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161 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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162 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
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163 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'