# HG changeset patch # User pavlo-lutsik # Date 1373051658 14400 # Node ID 05220e275e4b3285ca3b4551968d19537fcf68d0 # Parent 450c8ff1d11a76772733029a4a79627a98bd1b75 Deleted selected files diff -r 450c8ff1d11a -r 05220e275e4b RnBeadsGalaxy.R --- a/RnBeadsGalaxy.R Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,198 +0,0 @@ -#msg.file<-file("RnBeads.messages.out", open="w") -#sink(file=msg.file) - -suppressWarnings(suppressPackageStartupMessages(library(RnBeads))) -suppressWarnings(suppressPackageStartupMessages(library(getopt))) - -#all.opts<-names(rnb.options()) -opt.class<-RnBeads:::OPTION.TYPES[-28] -all.opts<-names(opt.class) -#all.opts<-paste("--", all.opts, sep="") -#all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE) -all.opts<-gsub("\\.","-", all.opts) -#opt.class<-sapply(rnb.options(), class) - -rnb.opt.spec<-data.frame( - Long=all.opts, - Short=as.character(1:length(all.opts)), - Mask=c(1,2)[as.integer((opt.class=="logical"))+1], - Type=opt.class) - -### automated xml file preparation -xml.strings<-apply(rnb.opt.spec,1, function(row){ - - opt.lab<-gsub("-", ".", row[1]) - opt.def.val<-rnb.getOption(opt.lab) - opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE) - tf.opt<-"\t\t\t\n\t\t\t" - opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ") - if(row[4]=="logical"){ - opt.type<-'select' - if(!is.null(opt.def.val) && opt.def.val) - opt.def.val<-"1" else - opt.def.val<-"0" - string<-sprintf("\t\t\n%s\n\t\t\n", opt.name, opt.type, opt.lab, opt.def.val, tf.opt) - }else{ - opt.type<-'text' - if(!is.null(opt.def.val) && opt.def.val!="") - opt.def.val<-paste(opt.def.val, collapse=",") else - opt.def.val<-"" - string<-sprintf("\t\t\n", opt.name, opt.type, opt.lab, opt.def.val) - } - string - }) - -cat(xml.strings, sep="", file="automated.settings.xml.txt") - -opt.def.strings<-apply(rnb.opt.spec,1, function(row){ - - opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE) - opt.long<-row[1] - opt.short<-row[2] - - if(row[4]=="logical"){ - def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long) - }else{ - def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name) - } - def.string - - }) -cat(opt.def.strings, sep="", file="automated.option.assignments.txt") - - -rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type) -rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type) -rnb.opt.spec<-rbind(data.frame( - Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","output-file", "report-dir"), - Short=c("d","s","a","i","f","g","e","b","p","r","o"), - Mask=c(1,2,2,2,2,2,2,2,2,1,1), - Type=c("character","character","character","character","character","character","character","character","character","character", "character")), - rnb.opt.spec) - -opts<-getopt(as.matrix(rnb.opt.spec)) -#opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2")) -print(opts) - -if(opts[["data-type"]]=="idatDir"){ - - data.source<-list() - data.type<-"idat.dir" - data.source[["idat.dir"]]<-opts[["idat-dir"]] - data.source[["sample.sheet"]]<-opts[["pheno"]] - -}else if(opts[["data-type"]]=="idatFiles"){ - - data.type<-"idat.dir" - file.string<-gsub(" ","", opts[["idat-files"]]) - files<-strsplit(file.string, ",")[[1]] - files<-files[files!=""] - bed.dir<-sprintf("%s_beds",opts[["report-dir"]]) - dir.create(bed.dir) - file.copy(files, bed.dir) - for(dat.file in list.files(bed.dir, full.names = TRUE)){ - file.rename(dat.file, gsub("\\.dat", ".bed", dat.file)) - } - data.source<-list() - data.source[["bed.dir"]]<-bed.dir - data.source[["sample.sheet"]]<-opts[["pheno"]] - - -}else if(opts[["data-type"]]=="GS.report"){ - - data.type<-"GS.report" - data.source<-opts[["gs-report"]] - -}else if(opts[["data-type"]]=="GEO"){ - - data.type<-"GEO" - data.source<-opts[["geo-series"]] - -}else if(opts[["data-type"]]=="data.files"){ - - data.type<-"GEO" - data.source<-opts[["geo-series"]] - -}else if(opts[["data-type"]]=="data.files"){ - - data.type<-"data.files" - data.source<-c(opts[["pheno"]], opts[["betas"]]) - if(!is.null(opts[["pvals"]])) - data.source<-c(data.source, opts[["pvals"]]) - -}else if(opts[["data-type"]]=="bed.dir"){ - - data.type<-"bed.dir" - file.string<-gsub(" ","", opts[["bed-files"]]) - files<-strsplit(file.string, ",")[[1]] - files<-files[files!=""] - bed.dir<-sprintf("%s_beds",opts[["report-dir"]]) - dir.create(bed.dir) - file.copy(files, bed.dir) - for(dat.file in list.files(bed.dir, full.names = TRUE)){ - file.rename(dat.file, gsub("\\.dat", ".bed", dat.file)) - } - data.source<-list() - data.source[["bed.dir"]]<-bed.dir - - logger.start(fname="NA") - sample.sheet<-rnb.read.annotation(opts[["pheno"]]) - logger.close() - if(length(files) < nrow(sample.sheet)) - stop("Not all bed files are present") - - cn<-colnames(sample.sheet) - dat.files<-sapply(strsplit(files, "\\/"), function(el) el[length(el)]) - sample.sheet<-cbind(sample.sheet, gsub("\\.dat", ".bed", dat.files)) - colnames(sample.sheet)<-c(cn, "BED_files") - data.source[["sample.sheet"]]<-sample.sheet -} - -if("logging" %in% names(opts)){ # TODO create a cleaner way of checking whether the full options set was supplied - - dump<-sapply(names(opt.class), function(on){ - getoptname<-gsub("-", "\\.","-",on) - if(getoptname %in% names(opts)){ - if(opt.class[on]=="logical"){ - ov<-TRUE - }else if(opt.class %in% c("character","character.vector")){ - ov<-opts[[getoptname]] - ov<-gsub("\"", "", ov) - if(opt.class=="character.vector"){ - ov<-as.character(strsplit(ov,",")) - } - - }else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){ - ov<-opts[[getoptname]] - ov<-gsub("\"", "", ov) - if(opt.class %in% c("integer.vector","numeric.vector")){ - ov<-as.character(strsplit(ov,",")) - } - } - eval(parse(text=sprintf("rnb.options(%s=ov)",on))) - } - }) - - logical.opts<-names(opt.class[opt.class=="logical"]) - logical.opts.false<-logical.opts[!logical.opts %in% gsub("-",".",names(opts))] - - - dump<-sapply(logical.opts.false, function(on){ - eval(parse(text=sprintf("rnb.options(%s=FALSE)",on))) - }) -} - -print(rnb.options()) - -#report.out.dir<-sprintf("%s_rnbReport", tempdir()) -report.out.dir<-opts[["report-dir"]] -print("Starting RnBeads with the following inputs:") -print(data.source) -print(report.out.dir) -print(data.type) -rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type) - - -#sink(file=NULL) -#flush(msg.file) -#close(msg.file) \ No newline at end of file diff -r 450c8ff1d11a -r 05220e275e4b install.rnbeads.R --- a/install.rnbeads.R Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -source("http://rnbeads.mpi-inf.mpg.de/install.R") \ No newline at end of file diff -r 450c8ff1d11a -r 05220e275e4b rnbeads.xml --- a/rnbeads.xml Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,506 +0,0 @@ - - - Performs RnBeads analysis for the selected set of - - R_SCRIPTS_PATH - R - - rnbeads_galaxy_wrapper.sh - --report-dir="$html_file.extra_files_path" - --output-file="$html_file" - #if str( $inputDataSelector.dataType ) == "idats" - --pheno="$inputDataSelector.sampleAnnotations" - #end if - #if str( $inputDataSelector.dataType ) != "idats" - #pass - #else if str( $inputDataSelector.idatSelector.idatSource ) == "history" - --data-type="idatFiles" - #set $idatList="" - #for $input_file in $inputDataSelector.idatSelector.idatSeries: - #set $idatList+=str( $input_file.idatFile ) - #set $idatList+="," - #end for - --idat-files="$idatList" - #else: - --data-type="idatDir" - --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path" - #end if - #if str( $inputDataSelector.dataType ) == "gsreport" - --data-type="GS.report" - --gs-report="$inputDataSelector.gsReportFile" - #end if - #if str( $inputDataSelector.dataType ) == "geo" - --data-type="GEO" - --geo-series=$inputDataSelector.geoSeries - #end if - #if str( $inputDataSelector.dataType ) == "tables" - --data-type="data.files" - --pheno="$inputDataSelector.sampleAnnotations" - #end if - #if str( $inputDataSelector.dataType ) == "tables" - --data-type="data.files" - --pheno="$inputDataSelector.sampleAnnotations" - --betas="$inputDataSelector.betaTable" - --pvals="$inputDataSelector.pvalTable" - #end if - #if str( $inputDataSelector.dataType ) == "bed" - --data-type="bed.dir" - --pheno="$inputDataSelector.sampleAnnotations" - #set $bedList="" - #for $input_file in $inputDataSelector.bedSeries: - #set $bedList+=str( $input_file.bedFile ) - #set $bedList+="," - #end for - --bed-files="$bedList" - #end if - #if str( $options.optionSet ) == "full" - #if str( $options.analysisName ) != "" - --analysis-name="$options.analysisName" - #end if - #if str( $options.logging ) == "True" - --logging - #end if - #if str( $options.email ) != "" - --email="$options.email" - #end if - #if str( $options.assembly ) != "" - --assembly="$options.assembly" - #end if - #if str( $options.columnsPairing ) != "" - --columns-pairing="$options.columnsPairing" - #end if - #if str( $options.analyzeSites ) == "True" - --analyze-sites - #end if - #if str( $options.regionTypes ) != "" - --region-types="$options.regionTypes" - #end if - #if str( $options.identifiersColumn ) != "" - --identifiers-column="$options.identifiersColumn" - #end if - #if str( $options.pointsCategory ) != "" - --points-category="$options.pointsCategory" - #end if - #if str( $options.colorsCategory ) != "" - --colors-category="$options.colorsCategory" - #end if - #if str( $options.colorsGradient ) != "" - --colors-gradient="$options.colorsGradient" - #end if - #if str( $options.minGroupSize ) != "" - --min-group-size="$options.minGroupSize" - #end if - #if str( $options.maxGroupCount ) != "" - --max-group-count="$options.maxGroupCount" - #end if - #if str( $options.gzLargeFiles ) == "True" - --gz-large-files - #end if - #if str( $options.strandSpecific ) == "True" - --strand-specific - #end if - #if str( $options.replicateIdColumn ) != "" - --replicate-id-column="$options.replicateIdColumn" - #end if - #if str( $options.loadingNormalization ) == "True" - --loading-normalization - #end if - #if str( $options.loadingDefaultDataType ) != "" - --loading-default-data-type="$options.loadingDefaultDataType" - #end if - #if str( $options.loadingTableSeparator ) != "" - --loading-table-separator="$options.loadingTableSeparator" - #end if - #if str( $options.loadingBedStyle ) != "" - --loading-bed-style="$options.loadingBedStyle" - #end if - #if str( $options.loadingBedColumns ) != "" - --loading-bed-columns="$options.loadingBedColumns" - #end if - #if str( $options.loadingBedFrameShift ) != "" - --loading-bed-frame-shift="$options.loadingBedFrameShift" - #end if - #if str( $options.normalizationMethod ) != "" - --normalization-method="$options.normalizationMethod" - #end if - #if str( $options.normalizationBackgroundMethod ) != "" - --normalization-background-method="$options.normalizationBackgroundMethod" - #end if - #if str( $options.qc ) == "True" - --qc - #end if - #if str( $options.qcBoxplots ) == "True" - --qc-boxplots - #end if - #if str( $options.qcBarplots ) == "True" - --qc-barplots - #end if - #if str( $options.qcSnpHeatmap ) == "True" - --qc-snp-heatmap - #end if - #if str( $options.qcSnpHeatmap ) == "True" - --qc-snp-heatmap - #end if - #if str( $options.qcSnpBoxplot ) == "True" - --qc-snp-boxplot - #end if - #if str( $options.qcSnpBarplot ) == "True" - --qc-snp-barplot - #end if - #if str( $options.qcSampleBatchSize ) != "" - --qc-sample-batch-size="$options.qcSampleBatchSize" - #end if - #if str( $options.filteringContextRemoval ) != "" - --filtering-context-removal="$options.filteringContextRemoval" - #end if - #if str( $options.filteringSnp ) == "True" - --filtering-snp - #end if - #if str( $options.filteringSnpFrequency ) != "" - --filtering-snp-frequency="$options.filteringSnpFrequency" - #end if - #if str( $options.filteringSnpAccepted ) != "" - --filtering-snp-accepted="$options.filteringSnpAccepted" - #end if - #if str( $options.filteringSexChromosomesRemoval ) == "True" - --filtering-sex-chromosomes-removal - #end if - #if str( $options.filteringMissingValueQuantile ) != "" - --filtering-missing-value-quantile="$options.filteringMissingValueQuantile" - #end if - #if str( $options.filteringCoverageThreshold ) != "" - --filtering-coverage-threshold="$options.filteringCoverageThreshold" - #end if - #if str( $options.filteringLowCoverageMasking ) == "True" - --filtering-low-coverage-masking - #end if - #if str( $options.filteringHighCoverageOutliers ) == "True" - --filtering-high-coverage-outliers - #end if - #if str( $options.filteringGreedycut ) == "True" - --filtering-greedycut - #end if - #if str( $options.filteringGreedycutPvalueThreshold ) != "" - --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" - #end if - #if str( $options.filteringGreedycutRcTies ) != "" - --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" - #end if - #if str( $options.filteringDeviationThreshold ) != "" - --filtering-deviation-threshold="$options.filteringDeviationThreshold" - #end if - #if str( $options.batch ) == "True" - --batch - #end if - #if str( $options.batchDreductionColumns ) != "" - --batch-dreduction-columns="$options.batchDreductionColumns" - #end if - #if str( $options.batchPrincipalComponents ) != "" - --batch-principal-components="$options.batchPrincipalComponents" - #end if - #if str( $options.batchCorrelationColumns ) != "" - --batch-correlation-columns="$options.batchCorrelationColumns" - #end if - #if str( $options.batchCorrelationPvalueThreshold ) != "" - --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" - #end if - #if str( $options.batchCorrelationPermutations ) != "" - --batch-correlation-permutations="$options.batchCorrelationPermutations" - #end if - #if str( $options.batchCorrelationQc ) == "True" - --batch-correlation-qc - #end if - #if str( $options.profiles ) == "True" - --profiles - #end if - #if str( $options.profilesBetaDistribution ) == "True" - --profiles-beta-distribution - #end if - #if str( $options.profilesIntersample ) == "True" - --profiles-intersample - #end if - #if str( $options.profilesDeviationPlots ) == "True" - --profiles-deviation-plots - #end if - #if str( $options.profilesColumns ) != "" - --profiles-columns="$options.profilesColumns" - #end if - #if str( $options.profilesClustering ) == "True" - --profiles-clustering - #end if - #if str( $options.profilesClusteringTopProbes ) != "" - --profiles-clustering-top-probes="$options.profilesClusteringTopProbes" - #end if - #if str( $options.regionProfilesTypes ) != "" - --region-profiles-types="$options.regionProfilesTypes" - #end if - #if str( $options.differential ) == "True" - --differential - #end if - #if str( $options.differentialPermutations ) != "" - --differential-permutations="$options.differentialPermutations" - #end if - #if str( $options.differentialComparisonColumns ) != "" - --differential-comparison-columns="$options.differentialComparisonColumns" - #end if - #if str( $options.differentialComparisonColumnsAllPairwise ) != "" - --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise" - #end if - #if str( $options.differentialEnrichment ) == "True" - --differential-enrichment - #end if - #if str( $options.exportToUcsc ) != "" - --export-to-ucsc="$options.exportToUcsc" - #end if - #if str( $options.exportToBed ) == "True" - --export-to-bed - #end if - #if str( $options.exportToCsv ) == "True" - --export-to-csv - #end if - #if str( $options.exportTypes ) != "" - --export-types="$options.exportTypes" - #end if - #if str( $options.colors3Gradient ) != "" - --colors-3-gradient="$options.colors3Gradient" - #end if - #if str( $options.loggingMemory ) == "True" - --logging-memory - #end if - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RnBeads is an R-package for comprehensive analysis of Illumina Infinium HumanMethylation450 BeadChip data. It extends previous approaches for this type of data analysis by high throughput capabilities, as well as presenting results in a comprehensive, highly interpretable fashion. - - - \ No newline at end of file diff -r 450c8ff1d11a -r 05220e275e4b rnbeads_galaxy_wrapper.sh --- a/rnbeads_galaxy_wrapper.sh Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -#!/bin/bash -random_hash=`tr -dc "[:alpha:]" < /dev/urandom | head -c 8` -Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads_${random_hash}.stdout 2>/tmp/rnbeads_${random_hash}.stderr -#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* -outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"` -echo $outfile -#outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"` - - -errl=`cat /tmp/rnbeads_${random_hash}.stderr | grep -e "[E|e]rror" | wc -l` -if [ "$errl" -gt 0 ] -then - cat /tmp/rnbeads_${random_hash}.stdout >&2 - #cat $outdir/analysis.log >&2 - cat /tmp/rnbeads_${random_hash}.stderr >&2 - exit 3 -else - echo "" >> $outfile - echo "RnBeads report" >> $outfile - echo "

Output was generated during the execution:
" >> $outfile - echo "
" >> outfile
-	cat /tmp/rnbeads_${random_hash}.stdout |sed -e "s/$//g" >> $outfile
-	echo "
" >> outfile - echo "

" >> $outfile - echo "" >> $outfile - exit 0 -fi \ No newline at end of file diff -r 450c8ff1d11a -r 05220e275e4b rnbeads_repos.txt.sample --- a/rnbeads_repos.txt.sample Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -repo1 Repository1 /data/iscan/idats \ No newline at end of file diff -r 450c8ff1d11a -r 05220e275e4b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - id, name, value - -
-
\ No newline at end of file diff -r 450c8ff1d11a -r 05220e275e4b tool_dependencies.xml --- a/tool_dependencies.xml Fri Jul 05 09:08:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ - - - - $REPOSITORY_INSTALL_DIR - - - - - http://CRAN.R-project.org/src/base/R-3/R-3.0.0.tar.gz - ./configure --prefix=$INSTALL_DIR --with-x=no - make - - $INSTALL_DIR/bin - - R --no-save <<< "install.packages("getopt"); source('http://rnbeads.mpi-inf.mpg.de')" - - - - You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. - - - \ No newline at end of file