# HG changeset patch
# User pavlo-lutsik
# Date 1373026664 14400
# Node ID 528511446522d7576bc173014292f11087fe5086
# Parent aad84663f9c2e1ee56dbcc3da821028fb7e5c7a8
Deleted selected files
diff -r aad84663f9c2 -r 528511446522 RnBeadsGalaxy.R
--- a/RnBeadsGalaxy.R Fri Jul 05 08:03:54 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 aad84663f9c2 -r 528511446522 faq.section.doc
Binary file faq.section.doc has changed
diff -r aad84663f9c2 -r 528511446522 galaxy.on.the.cloud
Binary file galaxy.on.the.cloud has changed
diff -r aad84663f9c2 -r 528511446522 galaxy_faq.docx
Binary file galaxy_faq.docx has changed
diff -r aad84663f9c2 -r 528511446522 install.rnbeads.R
--- a/install.rnbeads.R Fri Jul 05 08:03:54 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 aad84663f9c2 -r 528511446522 rnb.cloud.4.07.analysis.log
--- a/rnb.cloud.4.07.analysis.log Fri Jul 05 08:03:54 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,265 +0,0 @@
-2013-07-04 12:48:18 STATUS STARTED RnBeads Pipeline
-2013-07-04 12:48:18 INFO Initialized report index and saved to index.html
-2013-07-04 12:48:18 STATUS STARTED Loading Data
-2013-07-04 12:48:18 STATUS STARTED Loading GEO Data Series
-2013-07-04 12:53:38 INFO Loaded 1 data series from GSE38268
-2013-07-04 12:53:38 INFO Extracted 6 samples from series 1
-2013-07-04 12:53:38 INFO Parsed characteristics_ch1 sample information
-2013-07-04 12:53:38 STATUS COMPLETED Loading GEO Data Series
-2013-07-04 12:54:49 STATUS Loaded data from GSE38268. Output object is of class RnBeadSet
-2013-07-04 12:54:50 STATUS Added data loading section
-2013-07-04 12:54:50 STATUS COMPLETED Loading Data
-2013-07-04 12:54:50 STATUS STARTED Normalization
-2013-07-04 12:54:50 WARNING Incompatible values for object and method. Changed the normalization method to "none"
-2013-07-04 12:54:50 WARNING Incompatible values for object and background correction flag. Disabled the background correction
-2013-07-04 12:54:50 STATUS Performed normalization with method "swan"
-2013-07-04 12:54:53 STATUS Added normalization section
-2013-07-04 12:54:53 STATUS COMPLETED Normalization
-2013-07-04 12:54:54 INFO Initialized report index and saved to index.html
-2013-07-04 12:54:54 STATUS STARTED Quality Control
-2013-07-04 12:54:54 STATUS STARTED Quality Control Section
-2013-07-04 12:54:54 INFO No quality information present in the dataset
-2013-07-04 12:54:54 STATUS COMPLETED Quality Control Section
-2013-07-04 12:54:54 STATUS COMPLETED Quality Control
-2013-07-04 12:54:54 STATUS STARTED Visualizing Sample Mixups
-2013-07-04 12:54:54 STATUS STARTED Mixups Visualization Section
-2013-07-04 12:55:15 STATUS Added SNP heatmap
-2013-07-04 12:55:15 STATUS COMPLETED Mixups Visualization Section
-2013-07-04 12:55:15 STATUS COMPLETED Visualizing Sample Mixups
-2013-07-04 12:55:15 INFO Initialized report index and saved to index.html
-2013-07-04 12:55:15 STATUS STARTED Filtering
-2013-07-04 12:55:23 STATUS STARTED Probe Context Removal
-2013-07-04 12:56:00 STATUS Removed 3156 probe(s) out of context
-2013-07-04 12:56:01 STATUS Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_context.csv
-2013-07-04 12:56:01 STATUS Added a corresponding section to the report
-2013-07-04 12:56:01 STATUS COMPLETED Probe Context Removal
-2013-07-04 12:56:03 STATUS STARTED Removal of SNP-enriched Sites
-2013-07-04 12:56:38 STATUS Removed 18987 sites that overlap sites with more than 2 SNP(s)
-2013-07-04 12:56:38 STATUS Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_snp.csv
-2013-07-04 12:56:38 STATUS Added a corresponding section to the report
-2013-07-04 12:56:38 STATUS COMPLETED Removal of SNP-enriched Sites
-2013-07-04 12:56:39 INFO Omitting Greedycut because detection p-values are missing
-2013-07-04 12:56:42 STATUS STARTED Summary of Filtering Procedures
-2013-07-04 12:56:46 STATUS Added summary table of removed and retained values
-2013-07-04 12:57:47 STATUS Added comparison between removed and retained beta values
-2013-07-04 12:57:47 STATUS COMPLETED Summary of Filtering Procedures
-2013-07-04 12:57:47 STATUS COMPLETED Filtering
-2013-07-04 12:57:47 INFO Initialized report index and saved to index.html
-2013-07-04 12:57:47 STATUS STARTED Dimension Reduction Techniques
-2013-07-04 12:57:48 WARNING Removed 4301 loci ( sites ) because they contain missing values
-2013-07-04 12:57:49 STATUS Calculated PCA coordinates
-2013-07-04 12:57:49 STATUS Calculated MDS coordinates using manhattan distance
-2013-07-04 12:57:49 STATUS Calculated MDS coordinates using euclidean distance
-2013-07-04 12:57:50 WARNING Removed 491 loci ( tiling ) because they contain missing values
-2013-07-04 12:57:50 STATUS Calculated PCA coordinates
-2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
-2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
-2013-07-04 12:57:50 WARNING Removed 25 loci ( genes ) because they contain missing values
-2013-07-04 12:57:50 STATUS Calculated PCA coordinates
-2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
-2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
-2013-07-04 12:57:50 WARNING Removed 30 loci ( promoters ) because they contain missing values
-2013-07-04 12:57:50 STATUS Calculated PCA coordinates
-2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
-2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
-2013-07-04 12:57:51 WARNING Removed 15 loci ( cpgislands ) because they contain missing values
-2013-07-04 12:57:51 STATUS Calculated PCA coordinates
-2013-07-04 12:57:51 STATUS Calculated MDS coordinates using manhattan distance
-2013-07-04 12:57:51 STATUS Calculated MDS coordinates using euclidean distance
-2013-07-04 12:57:51 INFO Mapping 2 traits to point colors and types
-2013-07-04 13:14:59 INFO Principal components that explain at least 95 % of the total variance: 5
-2013-07-04 13:14:59 INFO Saved percentage of total variance to pca_variance_explained_1.csv
-2013-07-04 13:15:03 INFO Principal components that explain at least 95 % of the total variance: 5
-2013-07-04 13:15:03 INFO Saved percentage of total variance to pca_variance_explained_2.csv
-2013-07-04 13:15:08 INFO Principal components that explain at least 95 % of the total variance: 5
-2013-07-04 13:15:08 INFO Saved percentage of total variance to pca_variance_explained_3.csv
-2013-07-04 13:15:12 INFO Principal components that explain at least 95 % of the total variance: 5
-2013-07-04 13:15:12 INFO Saved percentage of total variance to pca_variance_explained_4.csv
-2013-07-04 13:15:16 INFO Principal components that explain at least 95 % of the total variance: 5
-2013-07-04 13:15:16 INFO Saved percentage of total variance to pca_variance_explained_5.csv
-2013-07-04 13:15:20 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations
-2013-07-04 13:15:20 STATUS COMPLETED Dimension Reduction Techniques
-2013-07-04 13:15:20 STATUS STARTED Tests for Associations
-2013-07-04 13:15:20 INFO Testing the following traits for associations: tumour site; tissue
-2013-07-04 13:15:20 STATUS Computed correlations between principal components and traits.
-2013-07-04 13:15:20 STATUS Computed pairwise correlations between traits.
-2013-07-04 13:15:20 STATUS COMPLETED Tests for Associations
-2013-07-04 13:15:48 STATUS STARTED Quality-associated Batch Effects
-2013-07-04 13:15:48 WARNING No quality information available
-2013-07-04 13:15:48 STATUS COMPLETED Quality-associated Batch Effects
-2013-07-04 13:15:48 INFO Initialized report index and saved to index.html
-2013-07-04 13:15:49 STATUS STARTED Methylation Profiles
-2013-07-04 13:15:49 INFO Designed color mappings for probe type and CGI status
-2013-07-04 13:15:57 STATUS STARTED Methylation Value Distributions - Sample Groups
-2013-07-04 13:19:31 STATUS COMPLETED Methylation Value Distributions - Sample Groups
-2013-07-04 13:19:31 STATUS STARTED Methylation Value Distributions - Probe Categories
-2013-07-04 13:22:46 STATUS COMPLETED Methylation Value Distributions - Probe Categories
-2013-07-04 13:22:47 STATUS STARTED Scatter Plots of Mean Beta vs Variance
-2013-07-04 13:22:47 INFO Sample subgroups are defined by: tumour site; tissue
-2013-07-04 13:22:48 WARNING Removed 10 loci with missing values in group all samples
-2013-07-04 13:31:43 WARNING Removed 1448 loci with missing values in group base of tongue (based on tumour site)
-2013-07-04 13:40:36 WARNING Removed 26 loci with missing values in group tonsil (based on tumour site)
-2013-07-04 13:49:33 WARNING Removed 56 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
-2013-07-04 13:58:28 WARNING Removed 78 loci with missing values in group HPV- HNSCC tumor (based on tissue)
-2013-07-04 14:07:20 STATUS Created 20 scatter plots of methylation variance on the site level
-2013-07-04 14:07:21 WARNING Removed 1 loci with missing values in group all samples
-2013-07-04 14:08:44 WARNING Removed 159 loci with missing values in group base of tongue (based on tumour site)
-2013-07-04 14:10:05 WARNING Removed 2 loci with missing values in group tonsil (based on tumour site)
-2013-07-04 14:11:26 WARNING Removed 4 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
-2013-07-04 14:12:48 WARNING Removed 7 loci with missing values in group HPV- HNSCC tumor (based on tissue)
-2013-07-04 14:14:34 WARNING Removed 9 loci with missing values in group base of tongue (based on tumour site)
-2013-07-04 14:16:42 WARNING Removed 8 loci with missing values in group base of tongue (based on tumour site)
-2013-07-04 14:17:34 WARNING Removed 1 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
-2013-07-04 14:18:49 WARNING Removed 2 loci with missing values in group base of tongue (based on tumour site)
-2013-07-04 14:20:26 STATUS Created 40 scatter plots of methylation variance on the region level
-2013-07-04 14:20:26 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance
-2013-07-04 14:20:26 STATUS STARTED Deviation Plots
-2013-07-04 14:49:08 STATUS Created 15 deviation plots on the site level
-2013-07-04 15:04:01 STATUS Created 20 deviation plots on the region level
-2013-07-04 15:04:02 STATUS Added summary table of variabilities
-2013-07-04 15:04:02 STATUS COMPLETED Deviation Plots
-2013-07-04 15:04:02 STATUS STARTED Sample Clustering
-2013-07-04 15:04:02 STATUS STARTED Agglomerative Hierarchical Clustering
-2013-07-04 15:04:02 STATUS Performed clustering on sites using correlation as a distance metric
-2013-07-04 15:04:02 STATUS Performed clustering on sites using manhattan as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on sites using euclidean as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on tiling using correlation as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on tiling using manhattan as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on tiling using euclidean as a distance metric
-2013-07-04 15:04:03 STATUS Completed clustering for tiling
-2013-07-04 15:04:03 STATUS Performed clustering on genes using correlation as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on genes using manhattan as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on genes using euclidean as a distance metric
-2013-07-04 15:04:03 STATUS Completed clustering for genes
-2013-07-04 15:04:03 STATUS Performed clustering on promoters using correlation as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on promoters using manhattan as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on promoters using euclidean as a distance metric
-2013-07-04 15:04:03 STATUS Completed clustering for promoters
-2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using correlation as a distance metric
-2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using manhattan as a distance metric
-2013-07-04 15:04:04 STATUS Performed clustering on cpgislands using euclidean as a distance metric
-2013-07-04 15:04:04 STATUS Completed clustering for cpgislands
-2013-07-04 15:04:04 STATUS COMPLETED Agglomerative Hierarchical Clustering
-2013-07-04 15:04:04 STATUS STARTED Clustering Section
-2013-07-04 15:04:05 STATUS STARTED Generating Heatmaps
-2013-07-04 15:04:05 STATUS STARTED Region type: sites
-2013-07-04 15:12:40 STATUS COMPLETED Region type: sites
-2013-07-04 15:12:40 STATUS STARTED Region type: tiling
-2013-07-04 15:21:19 STATUS COMPLETED Region type: tiling
-2013-07-04 15:21:19 STATUS STARTED Region type: genes
-2013-07-04 15:29:56 STATUS COMPLETED Region type: genes
-2013-07-04 15:29:56 STATUS STARTED Region type: promoters
-2013-07-04 15:38:33 STATUS COMPLETED Region type: promoters
-2013-07-04 15:38:33 STATUS STARTED Region type: cpgislands
-2013-07-04 15:47:09 STATUS COMPLETED Region type: cpgislands
-2013-07-04 15:47:10 STATUS Created 360 heatmaps based on the clustering results
-2013-07-04 15:47:10 STATUS COMPLETED Generating Heatmaps
-2013-07-04 15:47:10 STATUS STARTED Adding Color Legends
-2013-07-04 15:50:15 STATUS COMPLETED Adding Color Legends
-2013-07-04 15:50:15 STATUS STARTED Estimating Optimal Numbers of Clusters
-2013-07-04 15:51:21 STATUS Estimated number of clusters based on mean silhouette value
-2013-07-04 15:51:21 STATUS COMPLETED Estimating Optimal Numbers of Clusters
-2013-07-04 15:51:21 STATUS STARTED Overlapping Clusters with Sample Traits
-2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_1.csv
-2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_2.csv
-2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_3.csv
-2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_4.csv
-2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_5.csv
-2013-07-04 15:52:26 STATUS COMPLETED Overlapping Clusters with Sample Traits
-2013-07-04 15:52:26 STATUS COMPLETED Clustering Section
-2013-07-04 15:52:26 STATUS COMPLETED Sample Clustering
-2013-07-04 15:52:26 STATUS STARTED Regional Methylation Profiling
-2013-07-04 15:52:26 STATUS STARTED Computing Regional Profiles Based on Binning
-2013-07-04 15:52:26 STATUS STARTED Processing Region Type: genes
-2013-07-04 16:03:01 STATUS Set region annotation and site membership
-2013-07-04 16:04:02 STATUS Computed binned methylation values
-2013-07-04 16:04:02 STATUS COMPLETED Processing Region Type: genes
-2013-07-04 16:04:02 STATUS STARTED Processing Region Type: promoters
-2013-07-04 16:14:38 STATUS Set region annotation and site membership
-2013-07-04 16:15:29 STATUS Computed binned methylation values
-2013-07-04 16:15:29 STATUS COMPLETED Processing Region Type: promoters
-2013-07-04 16:15:29 STATUS STARTED Processing Region Type: cpgislands
-2013-07-04 16:25:46 STATUS Set region annotation and site membership
-2013-07-04 16:26:38 STATUS Computed binned methylation values
-2013-07-04 16:26:38 STATUS COMPLETED Processing Region Type: cpgislands
-2013-07-04 16:26:38 STATUS COMPLETED Computing Regional Profiles Based on Binning
-2013-07-04 16:26:38 STATUS STARTED Creating a Corresponding Section in the Report
-2013-07-04 16:26:38 STATUS Plotting region profiles for region genes and column tumour site ...
-2013-07-04 16:28:31 STATUS Plotting region profiles for region genes and column tissue ...
-2013-07-04 16:29:44 STATUS Plotting region profiles for region promoters and column tumour site ...
-2013-07-04 16:30:31 STATUS Plotting region profiles for region promoters and column tissue ...
-2013-07-04 16:31:15 STATUS Plotting region profiles for region cpgislands and column tumour site ...
-2013-07-04 16:32:16 STATUS Plotting region profiles for region cpgislands and column tissue ...
-2013-07-04 16:33:13 STATUS COMPLETED Creating a Corresponding Section in the Report
-2013-07-04 16:33:13 STATUS COMPLETED Regional Methylation Profiling
-2013-07-04 16:33:13 STATUS COMPLETED Methylation Profiles
-2013-07-04 16:33:13 INFO Initialized report index and saved to index.html
-2013-07-04 16:33:14 STATUS STARTED Differential Methylation - Analysis
-2013-07-04 16:33:14 INFO Using 0 permutation tests
-2013-07-04 16:33:14 INFO Using columns: title,geo_accession,status,submission_date,last_update_date,type,channel_count,source_name_ch1,organism_ch1,molecule_ch1,extract_protocol_ch1,label_ch1,label_protocol_ch1,taxid_ch1,hyb_protocol,scan_protocol,description,data_processing,platform_id,contact_name,contact_email,contact_laboratory,contact_department,contact_institute,contact_address,contact_city,contact_zip/postal_code,contact_country,supplementary_file,data_row_count,tumour site,tissue
-2013-07-04 16:33:14 INFO Using region types: tiling,genes,promoters,cpgislands
-2013-07-04 16:33:14 STATUS STARTED Comparison Information: tumour site
-2013-07-04 16:33:14 STATUS STARTED Comparing base of tongue-tonsil
-2013-07-04 16:33:14 STATUS STARTED Computing Differential Methylation Table (Site Level)
-2013-07-04 16:33:21 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 16:33:28 STATUS COMPLETED Computing Differential Methylation Table (Site Level)
-2013-07-04 16:33:28 STATUS STARTED Computing Differential Methylation Tables (Region Level)
-2013-07-04 16:45:21 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 16:45:21 STATUS Computed table for tiling
-2013-07-04 16:48:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 16:48:07 STATUS Computed table for genes
-2013-07-04 16:50:48 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 16:50:48 STATUS Computed table for promoters
-2013-07-04 16:53:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 16:53:07 STATUS Computed table for cpgislands
-2013-07-04 16:53:07 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
-2013-07-04 16:53:07 STATUS COMPLETED Comparing base of tongue-tonsil
-2013-07-04 16:53:07 STATUS COMPLETED Comparison Information: tumour site
-2013-07-04 16:53:07 STATUS STARTED Comparison Information: tissue
-2013-07-04 16:53:07 STATUS STARTED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
-2013-07-04 16:53:07 STATUS STARTED Computing Differential Methylation Table (Site Level)
-2013-07-04 16:53:12 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 16:53:17 STATUS COMPLETED Computing Differential Methylation Table (Site Level)
-2013-07-04 16:53:17 STATUS STARTED Computing Differential Methylation Tables (Region Level)
-2013-07-04 17:04:12 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 17:04:13 STATUS Computed table for tiling
-2013-07-04 17:06:56 STATUS Computed table for genes
-2013-07-04 17:09:29 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
-2013-07-04 17:09:29 STATUS Computed table for promoters
-2013-07-04 17:11:43 STATUS Computed table for cpgislands
-2013-07-04 17:11:43 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
-2013-07-04 17:11:43 STATUS COMPLETED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
-2013-07-04 17:11:43 STATUS COMPLETED Comparison Information: tissue
-2013-07-04 17:11:43 INFO Skipping enrichment analysis of differentially methylated regions
-2013-07-04 17:11:43 STATUS COMPLETED Differential Methylation - Analysis
-2013-07-04 17:11:43 STATUS STARTED Differential Methylation - Report Generation
-2013-07-04 17:11:43 STATUS Added introductory section
-2013-07-04 17:11:43 STATUS STARTED Adding Site Level Information
-2013-07-04 18:03:20 STATUS COMPLETED Adding Site Level Information
-2013-07-04 18:03:20 STATUS STARTED Adding Region Level Information
-2013-07-04 18:31:24 STATUS COMPLETED Adding Region Level Information
-2013-07-04 18:31:24 STATUS COMPLETED Differential Methylation - Report Generation
-2013-07-04 18:31:25 INFO Initialized report index and saved to index.html
-2013-07-04 18:31:25 STATUS STARTED Data Export
-2013-07-04 18:31:25 STATUS STARTED Exporting RnBSet
-2013-07-04 18:31:25 STATUS STARTED Exporting sites
-2013-07-04 18:31:25 STATUS STARTED Creating UCSC Track Hub -- bigBed
-2013-07-04 18:31:25 STATUS STARTED Conversion to BED
-2013-07-04 18:33:46 STATUS COMPLETED Conversion to BED
-2013-07-04 18:33:46 STATUS STARTED Creating UCSC Track Hub
-2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub
-2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub -- bigBed
-2013-07-04 18:34:06 STATUS STARTED Creating UCSC Track Hub -- bigWig
-2013-07-04 18:34:06 STATUS STARTED Conversion to bedGraph
-2013-07-04 18:36:10 STATUS COMPLETED Conversion to bedGraph
-2013-07-04 18:36:10 STATUS STARTED Creating UCSC Track Hub
-2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub
-2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub -- bigWig
-2013-07-04 18:36:28 STATUS COMPLETED Exporting sites
-2013-07-04 18:36:28 STATUS COMPLETED Exporting RnBSet
-2013-07-04 18:36:28 STATUS STARTED Writing export report
-2013-07-04 18:36:28 STATUS COMPLETED Writing export report
-2013-07-04 18:36:28 STATUS COMPLETED Data Export
-2013-07-04 18:36:28 INFO Initialized report index and saved to index.html
-2013-07-04 18:36:29 STATUS COMPLETED RnBeads Pipeline
-
diff -r aad84663f9c2 -r 528511446522 rnbeads.xml
--- a/rnbeads.xml Fri Jul 05 08:03:54 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,506 +0,0 @@
-
-
" >> outfile - cat /tmp/rnbeads.stdout |sed -e "s/$/" >> outfile - echo "" >> $outfile - echo "" >> $outfile - exit 0 -fi \ No newline at end of file diff -r aad84663f9c2 -r 528511446522 rnbeads_repos.txt.sample --- a/rnbeads_repos.txt.sample Fri Jul 05 08:03:54 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 aad84663f9c2 -r 528511446522 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -
/g" >> $outfile - echo "