Mercurial > repos > saskia-hiltemann > mothur_align_check

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author saskia-hiltemann
date Tue, 07 Jun 2016 10:47:17 -0400
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48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
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1 Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
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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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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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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)
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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155 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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156 --datasetid='2578'
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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157 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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158 --new_file_path='$__new_file_path__'
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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159 # specifies files to copy to the new_file_path
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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160 # The list is separated by commas
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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161 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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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
48b3a755bd02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
saskia-hiltemann
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163 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'