Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

annotate data_manager/customProDB_annotation.R @ 12:1ebf39dd0dca draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e9e2b5f5d422c1ff2f4db1ef83eb585ae3815517
author galaxyp
date Mon, 26 Jun 2017 17:13:02 -0400
parents 63c48a6eddb6
children e7766dd218d9
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1 #!/usr/bin/env Rscript
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3 initial.options <- commandArgs(trailingOnly = FALSE)
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4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
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6 ## begin warning handler
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7 withCallingHandlers({
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9 library(methods) # Because Rscript does not always do this
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11 options('useFancyQuotes' = FALSE)
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13 suppressPackageStartupMessages(library("optparse"))
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14 suppressPackageStartupMessages(library("RGalaxy"))
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15 suppressPackageStartupMessages(library("GetoptLong"))
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18 option_list <- list()
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19 option_list$dbkey <- make_option('--dbkey', type='character')
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20 option_list$ensembl_host <- make_option('--ensembl_host', type='character')
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21 option_list$ensembl_dataset <- make_option('--ensembl_dataset', type='character')
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22 option_list$dbsnp <- make_option('--dbsnp', type='character')
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23 option_list$cosmic <- make_option('--cosmic', type='logical')
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24 option_list$outputFile <- make_option('--outputFile', type='character')
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25 option_list$dbkey_description <- make_option('--dbkey_description', type='character')
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27 opt <- parse_args(OptionParser(option_list=option_list))
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30 customProDB_annotation <- function(
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31 dbkey = GalaxyCharacterParam(required=FALSE),
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32 ensembl_host = GalaxyCharacterParam(required=FALSE),
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33 ensembl_dataset = GalaxyCharacterParam(required=FALSE),
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34 dbsnp_str = GalaxyCharacterParam(required=FALSE),
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35 cosmic = GalaxyLogicalParam(required=FALSE),
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36 dbkey_description = GalaxyCharacterParam(required=FALSE),
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37 outputFile = GalaxyOutput("output","json"))
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38 {
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39 options(stringsAsFactors = FALSE, gsubfn.engine = "R")
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40
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41 if (!file.exists(outputFile))
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42 {
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43 gstop("json params file does not exist")
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44 }
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45
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46 if (length(dbkey)+length(ensembl_dataset)+length(ensembl_host) == 0)
9
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47 {
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48 gstop("one of the genome annotation sources must be specified; either dbkey or host and dataset")
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49 }
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50 else if (length(dbkey) > 0 &&
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51 (length(ensembl_dataset) > 0 || length(ensembl_host) > 0))
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52 {
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53 gstop("only one genome annotation source can be specified; either dbkey or host and dataset")
9
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54 }
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56 if (length(dbsnp_str) > 0)
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57 {
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58 dbsnp = dbsnp_str
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59 }
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60 else
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61 {
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62 dbsnp = NULL
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63 }
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64
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65 use_cosmic = FALSE
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66 if (length(cosmic) > 0)
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67 {
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68 if (length(dbkey) > 0 && grepl("^hg", dbkey) ||
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69 length(ensembl_dataset) > 0 && grepl("^hsapiens", ensembl_dataset))
9
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70 {
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71 use_cosmic = TRUE
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72 }
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73 else
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74 {
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75 gstop("COSMIC annotation requested but dbkey does not indicate a human genome (e.g. hg19)")
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76 }
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77 }
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78
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79 suppressPackageStartupMessages(library(rjson))
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80 params = fromJSON(file=outputFile)
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81 target_directory = params$output_data[[1]]$extra_files_path
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82 dir.create(target_directory)
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83
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84 tryCatch(
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85 {
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86 file.remove(outputFile)
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87 }, error=function(err)
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88 {
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89 gstop("failed to remove json params file after reading")
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90 })
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91
11
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92 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
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93 download.file("https://github.com/chambm/customProDB/archive/c57e5498392197bc598a18c26acb70d7530a921c.zip", "customProDB.zip", quiet=TRUE)
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94 unzip("customProDB.zip")
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95 devtools::load_all("customProDB-c57e5498392197bc598a18c26acb70d7530a921c")
9
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96
11
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97 #suppressPackageStartupMessages(library(customProDB))
9
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98 options(timeout=3600)
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99
11
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100 # download protein and coding sequences for UCSC annotation
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101 if (length(dbkey) > 0)
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102 {
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103 proteinFastaFilepath = paste(dbkey, ".protein.fa", sep="")
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104
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105 cat(paste("Downloading protein FASTA from:", getProteinFastaUrlFromUCSC(dbkey), "\n"))
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106 download.file(getProteinFastaUrlFromUCSC(dbkey), proteinFastaFilepath, quiet=T, mode='wb')
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107
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108 local_cache_path = paste0("customProDB_annotation_", dbkey, "-", tools::md5sum(proteinFastaFilepath)[[1]])
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109 codingFastaFilepath = paste0(local_cache_path, "/", dbkey, ".cds.fa")
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110 dir.create(local_cache_path, showWarnings=FALSE)
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111
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112 if (!file.exists(codingFastaFilepath)) {
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113 cat(paste("Downloading coding FASTA from:", getCodingFastaUrlFromUCSC(dbkey), "\n"))
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114 download.file(getCodingFastaUrlFromUCSC(dbkey), codingFastaFilepath, quiet=T, mode='wb')
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115 }
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116
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117 cat(paste("Preparing Refseq annotation files\n"))
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118 PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic, local_cache_path=local_cache_path)
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119
11
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120 if (length(dbkey_description) < 1)
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121 {
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122 dbkey_description = dbkey
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123 }
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124 }
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125 else
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126 {
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127 local_cache_path = paste0("customProDB_annotation_", ensembl_dataset, "_", ensembl_host)
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128
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129 suppressPackageStartupMessages(library(biomaRt))
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130 cat(paste("Preparing Ensembl annotation files\n"))
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131 ensembl_mart = useMart("ENSEMBL_MART_ENSEMBL", dataset=ensembl_dataset, host=ensembl_host)
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132 PrepareAnnotationEnsembl(mart=ensembl_mart, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic, local_cache_path=local_cache_path)
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133
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134 metadata = sqldf::sqldf("SELECT value FROM metadata WHERE name='BioMart database version' OR name='BioMart dataset description' OR name='BioMart dataset version'",
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135 dbname=file.path(target_directory, "txdb.sqlite"))
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136 version = metadata$value[1] # Ensembl Genes 87
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137 assembly = metadata$value[3]
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138 dbkey = paste0(ensembl_dataset, "_", sub(".*?(\\d+)", "\\1", version, perl=TRUE))
9
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139
11
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140 # convert Ensembl chromosome names to UCSC for Galaxy compatibility
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141 chromosomeMappingsBaseUrl = "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master"
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142 assemblyNoGrcPatch = sub("(\\S+?)(\\.p\\S+)?$", "\\1", assembly, perl=TRUE)
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143 chromosomeMappingsUrl = qq("@{chromosomeMappingsBaseUrl}/@{assemblyNoGrcPatch}_ensembl2UCSC.txt")
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144 if (RCurl::url.exists(chromosomeMappingsUrl))
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145 {
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146 cat(qq("Converting Ensembl chromosome names from: @{chromosomeMappingsUrl}\n"))
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147 e2u = read.delim(chromosomeMappingsUrl, header=FALSE, col.names=c("ensembl", "ucsc"))
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148 e2u = setNames(as.list(e2u$ucsc), e2u$ensembl)
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149 load(file.path(target_directory, "exon_anno.RData"))
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150 exon$chromosome_name = sapply(exon$chromosome_name, function(x) e2u[[as.character(x)]])
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151 exon = exon[nzchar(exon$chromosome_name), ] # omit genome patches with no mapping
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152 save(exon, file=file.path(target_directory, "exon_anno.RData"))
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153 }
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154 else
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155 {
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156 gwarning(qq("unable to convert Ensembl chromosome names to UCSC; mapping file @{assemblyNoGrcPatch}_ensembl2UCSC.txt does not exist"))
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157 }
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158
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159 if (length(dbkey_description) < 1)
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160 {
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161 dbkey_description = qq("@{ensembl_dataset} (@{version}) (@{assembly})")
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162 }
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163 }
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164
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165 qualified_dbkey = dbkey
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166
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167 if (length(dbsnp_str) > 0 && nzchar(dbsnp_str))
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168 {
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169 qualified_dbkey = qq("@{qualified_dbkey}_db@{dbsnp_str}")
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170 dbkey_description = qq("@{dbkey_description} (db@{dbsnp_str})")
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171 }
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172
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173 if (length(cosmic) > 0)
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174 {
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175 qualified_dbkey = qq("@{qualified_dbkey}_cosmic")
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176 dbkey_description = qq("@{dbkey_description} (COSMIC)")
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177 }
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178
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179 outputPath = paste0(qualified_dbkey, "/customProDB")
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180 output = list(data_tables = list())
11
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181 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=qualified_dbkey, value=qualified_dbkey)
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182 write(toJSON(output), file=outputFile)
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183 }
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184
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185
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186 params <- list()
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187 for(param in names(opt))
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188 {
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189 if (!param == "help")
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190 params[param] <- opt[param]
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191 }
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192
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193 setClass("GalaxyRemoteError", contains="character")
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194 wrappedFunction <- function(f)
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195 {
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196 tryCatch(do.call(f, params),
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197 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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198 }
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199
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200
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201 suppressPackageStartupMessages(library(RGalaxy))
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202 do.call(customProDB_annotation, params)
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203
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204 ## end warning handler
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205 }, warning = function(w) {
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206 cat(paste("Warning:", conditionMessage(w), "\n"))
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207 invokeRestart("muffleWarning")
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208 })