diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 12d844c4d..a8db12607 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -10,14 +10,10 @@ import java.util.regex.Matcher repositories { mavenCentral() - // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk - maven { - url "https://clojars.org/repo" - } - // Added for org.clojars.chapmanb:sam - maven { - url "https://maven.scijava.org/content/groups/public" - } + // Added for jhdf5 from FASTQC / sequence analysis module +// maven { +// url "https://maven.scijava.org/content/groups/public/" +// } } configurations.all { @@ -96,16 +92,30 @@ dependencies { ) ) + // NOTE: this maven repo has been unreliable +// BuildUtils.addExternalDependency( +// project, +// new ExternalDependency( +// 'cisd:jhdf5:19.04.1', +// 'JHDF5', +// 'JHDF5', +// 'https://unlimited.ethz.ch/display/JHDF/', +// ExternalDependency.BSD_LICENSE_NAME, +// ExternalDependency.BSD_LICENSE_URL, +// 'JHDF5 is a Java binding for HDF5. Used by FastQC' +// ) +// ) + BuildUtils.addExternalDependency( project, new ExternalDependency( - 'org.clojars.chapmanb:sam:1.96', - 'picard tools', - 'picard tools', - 'http://sourceforge.net/projects/picard/', + 'net.iharder:base64:2.3.8', + 'Base64', + 'Base64', + 'http://iharder.net/base64/', ExternalDependency.MIT_LICENSE_NAME, ExternalDependency.MIT_LICENSE_URL, - 'Library for working with SAM/BAM files. Used by FastQC' + 'Library for Base64 encoding. Used by FastQC' ) ) implementation "net.sf.opencsv:opencsv:${opencsvVersion}" diff --git a/SequenceAnalysis/resources/external/basicHistogram.r b/SequenceAnalysis/resources/external/basicHistogram.r deleted file mode 100644 index 7e9e1fc10..000000000 --- a/SequenceAnalysis/resources/external/basicHistogram.r +++ /dev/null @@ -1,62 +0,0 @@ -options(warn = -1) - -library(reshape) -library(lattice) -library(plyr) -library(ggplot2) -library(grid) -library(perm) -library(gridExtra) -library(naturalsort) - -library(getopt); -library(Matrix); - -options(scipen=1000000000) - -spec <- matrix(c( - 'inputFile', 'i', 1, "character", - 'outputFile', 'o', 1, "character", - 'plotTitle', 't', 2, "character", - 'xLabel', NA, 2, "character", - 'colIdx', 'c', 1, "integer", - 'binWidth', NA, 2, "integer", - 'maxValue', NA, 2, "integer", - 'hasHeaders', 'h', 2, "logical" -), ncol=4, byrow=TRUE); -opts = getopt(spec, commandArgs(trailingOnly = TRUE)); - -if ( is.null(opts$xLabel ) ) { opts$xLabel = "" } -if ( is.null(opts$plotTitle ) ) { opts$plotTitle = "" } -if ( is.null(opts$hasHeaders ) ) { opts$hasHeaders = TRUE } - -df <- read.table(opts$inputFile, quote="\"", header = opts$hasHeaders); - -#echo "Generating Histogram" - -colName <-names(df)[opts$colIdx]; - -if ( !is.null(opts$maxValue)) { - message(paste0("combining all values greater than: ", opts$maxValue)); - - df[colName][df[colName] > opts$maxValue] <- opts$maxValue -} - -P<-ggplot(df,aes_string(x=colName)) + - ggtitle(opts$plotTitle) + - #scale_y_continuous(limits=c(0,2),labels=c("0.0","0.5","1.0","1.5","2.0")) + - geom_histogram(binwidth = opts$binWidth) + - theme( - #axis.text.x = element_blank(), - plot.margin = unit(c(0.3,0.3,0.3,0.3),"in"), - plot.title = element_text(size=14,vjust=2), - axis.title.x = element_text(size=14,vjust=-1), - axis.title.y = element_text(size=14,vjust=2), - strip.text.x = element_text(size = 12,face="bold")) + - xlab(opts$xLabel) + - ylab("Count") - - -png(opts$outputFile,width=880, height=680) -print(P); -dev.off(); \ No newline at end of file diff --git a/SequenceAnalysis/resources/external/basicScatter.r b/SequenceAnalysis/resources/external/basicScatter.r deleted file mode 100644 index 5789b4cee..000000000 --- a/SequenceAnalysis/resources/external/basicScatter.r +++ /dev/null @@ -1,55 +0,0 @@ -options(warn = -1) - -library(reshape) -library(lattice) -library(plyr) -library(ggplot2) -library(grid) -library(perm) -library(gridExtra) -library(naturalsort) - -library(getopt); -library(Matrix); - -options(scipen=1000000000) - -spec <- matrix(c( - 'inputFile', 'i', 1, "character", - 'outputFile', 'o', 1, "character", - 'plotTitle', 't', 2, "character", - 'xLabel', NA, 2, "character", - 'xColIdx', 'x', 1, "integer", - 'yColIdx', 'y', 1, "integer", - 'hasHeaders', 'h', 2, "logical" -), ncol=4, byrow=TRUE); -opts = getopt(spec, commandArgs(trailingOnly = TRUE)); - -if ( is.null(opts$xLabel ) ) { opts$xLabel = "" } -if ( is.null(opts$plotTitle ) ) { opts$plotTitle = "" } -if ( is.null(opts$hasHeaders ) ) { opts$hasHeaders = TRUE } - -df <- read.table(opts$inputFile, quote="\"", header = opts$hasHeaders); - -#echo "Generating Plot" - -xColName <-names(df)[opts$xColIdx]; -yColName <-names(df)[opts$yColIdx]; - -P<-ggplot(df,aes_string(x=xColName, y=yColName)) + - ggtitle(opts$plotTitle) + - geom_point(shape=1) + - theme( - #axis.text.x = element_blank(), - plot.margin = unit(c(0.3,0.3,0.3,0.3),"in"), - plot.title = element_text(size=14,vjust=2), - axis.title.x = element_text(size=14,vjust=-1), - axis.title.y = element_text(size=14,vjust=2), - strip.text.x = element_text(size = 12,face="bold")) + - xlab(opts$xLabel) + - ylab("Count") - - -png(opts$outputFile,width=880, height=680) -print(P); -dev.off(); \ No newline at end of file diff --git a/SequenceAnalysis/resources/external/cisd-jhdf5.jar b/SequenceAnalysis/resources/external/cisd-jhdf5.jar new file mode 100644 index 000000000..2c05d6abb Binary files /dev/null and b/SequenceAnalysis/resources/external/cisd-jhdf5.jar differ diff --git a/SequenceAnalysis/resources/external/coverageGraph.r b/SequenceAnalysis/resources/external/coverageGraph.r deleted file mode 100644 index 2fb7af566..000000000 --- a/SequenceAnalysis/resources/external/coverageGraph.r +++ /dev/null @@ -1,64 +0,0 @@ -library(reshape) -library(lattice) -library(plyr) -library(ggplot2) -library(grid) -library(perm) -library(gridExtra) -library(naturalsort) - -library(getopt); -library(Matrix); - -spec <- matrix(c( - 'colHeader', '-c', 1, "character", - 'outputFile', '-o', 1, "character", - 'inputFile', '-i', 1, "character", - 'plotTitle', '-t', 1, "character", - 'vertical', '-v', 1, "integer", - 'yLabel', NA, 1, "character" -), ncol=4, byrow=TRUE); -opts = getopt(spec, commandArgs(trailingOnly = TRUE)); -if ( is.null(opts$vertical ) ) { opts$vertical = 0 } - -df <- read.table(opts$inputFile, quote="\"", header = TRUE, fill = TRUE, na.strings = "NA"); -df$SequenceName <- factor(df$SequenceName, levels = naturalsort(unique(df$SequenceName))); - -df <- df[(!is.na(df[opts$colHeader])),]; -#str(df) - -plotHeight <- 680; - -if (opts$vertical == 1){ - facet1 <- 'SequenceName'; - facet2 <- '.'; - fac_formula <- as.formula(paste(facet1,"~",facet2)) - facetLine <- facet_grid(fac_formula, scales="free", space="fixed") - - plotHeight <- (500 * nlevels(df$SequenceName)); -} else { - facet1 <- '.'; - facet2 <- 'SequenceName'; - fac_formula <- as.formula(paste(facet1,"~",facet2)) - facetLine <- facet_grid(fac_formula, scales="free", space="free") -} - -# make all chroms plot -P<-ggplot(df,aes_string(x="Start",y=opts$colHeader)) + - ggtitle(opts$plotTitle) + - #scale_y_continuous(limits=c(0,2),labels=c("0.0","0.5","1.0","1.5","2.0")) + - geom_point(stat='identity') + - theme(axis.text.x = element_blank(), - plot.margin = unit(c(0.3,0.3,0.3,0.3),"in"), - plot.title = element_text(size=14,vjust=2), - axis.title.x = element_text(size=14,vjust=-1), - axis.title.y = element_text(size=14,vjust=2), - strip.text.x = element_text(size = 12,face="bold")) + - xlab("Position") + - ylab(opts$yLabel) + - facetLine - - -png(opts$outputFile,width=880, height=plotHeight) -print(P); -dev.off(); \ No newline at end of file diff --git a/SequenceAnalysis/resources/external/fastqc/Configuration/adapter_list.txt b/SequenceAnalysis/resources/external/fastqc/Configuration/adapter_list.txt index 63d7ff601..236dca897 100644 --- a/SequenceAnalysis/resources/external/fastqc/Configuration/adapter_list.txt +++ b/SequenceAnalysis/resources/external/fastqc/Configuration/adapter_list.txt @@ -20,5 +20,8 @@ # fragments for now. Illumina Universal Adapter AGATCGGAAGAG -Illumina Small RNA Adapter ATGGAATTCTCG -Nextera Transposase Sequence CTGTCTCTTATA \ No newline at end of file +Illumina Small RNA 3' Adapter TGGAATTCTCGG +Illumina Small RNA 5' Adapter GATCGTCGGACT +Nextera Transposase Sequence CTGTCTCTTATA +PolyA AAAAAAAAAAAA +PolyG GGGGGGGGGGGG \ No newline at end of file diff --git a/SequenceAnalysis/resources/external/fastqc/Configuration/contaminant_list.txt b/SequenceAnalysis/resources/external/fastqc/Configuration/contaminant_list.txt index eb4b70a83..1ae0bd980 100644 --- a/SequenceAnalysis/resources/external/fastqc/Configuration/contaminant_list.txt +++ b/SequenceAnalysis/resources/external/fastqc/Configuration/contaminant_list.txt @@ -43,7 +43,6 @@ Illumina NlaIII expression Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG Illumina Small RNA Adapter 1 GTTCAGAGTTCTACAGTCCGACGATC Illumina Small RNA Adapter 2 TGGAATTCTCGGGTGCCAAGG Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA -Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC @@ -84,14 +83,11 @@ Illumina NlaIII Gex PCR Primer 1 CAAGCAGAAGACGGCATACGA Illumina NlaIII Gex PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA Illumina NlaIII Gex Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG -Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA Illumina 5p RNA Adapter GTTCAGAGTTCTACAGTCCGACGATC Illumina RNA Adapter1 TGGAATTCTCGGGTGCCAAGG Illumina Small RNA 3p Adapter 1 ATCTCGTATGCCGTCTTCTGCTTG Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA -Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA -Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC TruSeq Universal Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT TruSeq Adapter, Index 1 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG @@ -115,7 +111,7 @@ TruSeq Adapter, Index 19 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACTCTCGTATGC TruSeq Adapter, Index 20 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 21 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGTCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 22 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTTCTCGTATGCCGTCTTCTGCTTG -TruSeq Adapter, Index 23 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTTCTCGTATGCCGTCTTCTGCTTG +TruSeq Adapter, Index 23 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCACTCTTCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 25 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 27 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTCTCGTATGCCGTCTTCTGCTTG @@ -180,3 +176,11 @@ ABI Solid3 EF1 alpha Sense Primer CATGTGTGTTGAGAGCTTC ABI Solid3 EF1 alpha Antisense Primer GAAAACCAAAGTGGTCCAC ABI Solid3 GAPDH Forward Primer TTAGCACCCCTGGCCAAGG ABI Solid3 GAPDH Reverse Primer CTTACTCCTTGGAGGCCATG + + + +Clontech Universal Primer Mix Short CTAATACGACTCACTATAGGGC +Clontech Universal Primer Mix Long CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGT +Clontech SMARTer II A Oligonucleotide AAGCAGTGGTATCAACGCAGAGTAC +Clontech SMART CDS Primer II A AAGCAGTGGTATCAACGCAGAGTACT + diff --git a/SequenceAnalysis/resources/external/fastqc/Configuration/limits.txt b/SequenceAnalysis/resources/external/fastqc/Configuration/limits.txt index 742d172cc..ec4280c1a 100644 --- a/SequenceAnalysis/resources/external/fastqc/Configuration/limits.txt +++ b/SequenceAnalysis/resources/external/fastqc/Configuration/limits.txt @@ -2,7 +2,7 @@ # module at all by setting the value below to 1 for the # modules you want to remove. duplication ignore 0 -kmer ignore 0 +kmer ignore 1 n_content ignore 0 overrepresented ignore 0 quality_base ignore 0 diff --git a/SequenceAnalysis/resources/external/fastqc/INSTALL.txt b/SequenceAnalysis/resources/external/fastqc/INSTALL.txt deleted file mode 100644 index f55db8b08..000000000 --- a/SequenceAnalysis/resources/external/fastqc/INSTALL.txt +++ /dev/null @@ -1,127 +0,0 @@ -Installing FastQC -------------------- -FastQC is a java application. In order to run it needs your system to have a suitable -Java Runtime Environment (JRE) installed. Before you try to run FastQC you should therefore -ensure that you have a suitable JRE. There are a number of different JREs available -however the one we have tested is the v1.6 JRE from Oracle. This is available -for a number of different platforms from www.java.com (click the download now button at the -top). - -If you're not sure whether you have java installed then you can test this from a command -prompt. To get a command prompt try: - -Windows: Select Start > Run, and type 'cmd' (no quotes) in the box which appears, press OK - -MaxOSX: Run Applications > Utilities > Terminal - -Linux: From your applications menu look for an application called 'Terminal' or 'Konsole'. -Either of these will give you a usable shell. - -At the command prompt type 'java -version' and press enter. You should see something like: - -java version "1.6.0_17" -Java(TM) SE Runtime Environment (build 1.6.0_17-b04-248-10M3025) -Java HotSpot(TM) Client VM (build 14.3-b01-101, mixed mode) - -If you get an error then you don't have java installed. If the version listed on the first -line is less than 1.5 then you might have problems running FastQC. - -Actually installing FastQC is as simple as unzipping the zip file it comes in into a -suitable location. That's it. Once unzipped it's ready to go. - -Running FastQC --------------- - -You can run FastQC in one of two modes, either as an interactive graphical application -in which you can dynamically load FastQ files and view their results. - -Alternatively you can run FastQC in a non-interactive mode where you specify the files -you want to process on the command line and FastQC will generate an HTML report for -each file without launching a user interface. This would allow FastQC to be run as -part of an analysis pipeline. - - -Running FastQC Interactively ----------------------------- -Windows: Simply double click on the run_fastqc bat file. If you want to make a pretty -shortcut then we've included an icon file in the top level directory so you don't have -to use the generic bat file icon. - -MacOSX: There is an application bundle for MacOSX which you can use to install and run -FastQC. Just drag the application from the disk image to your Applications folder (or -wherever you want to install the program). - -Linux: We have included a wrapper script, called 'fastqc' which is the easiest way to -start the program. The wrapper is in the top level of the FastQC installation. You -may need to make this file executable: - -chmod 755 fastqc - -..but once you have done that you can run it directly - -./fastqc - -..or place a link in /usr/local/bin to be able to run the program from any location: - -sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc - - -Running FastQC as part of a pipeline ------------------------------------- -To run FastQC non-interactively you should use the fastqc wrapper script to launch -the program. You will probably want to use the zipped install file on every platform -(even OSX). - -To run non-interactively you simply have to specify a list of files to process -on the commandline - -fastqc somefile.txt someotherfile.txt - -You can specify as many files to process in a single run as you like. If you don't -specify any files to process the program will try to open the interactive application -which may result in an error if you're running in a non-graphical environment. - -There are a few extra options you can specify when running non-interactively. Full -details of these can be found by running - -fastqc --help - -By default, in non-interactive mode FastQC will create both a zipped copy of the -QC report, and also extract this to create a folder which contains the report -files ready to be viewed. If you only want to create the zipped file then you can -add - ---noextract - -To the launch command to suppress the unzipping. - -If you want to save your reports in a folder other than the folder which contained -your original FastQ files then you can specify an alternative location by setting a ---outdir value: - ---outdir=/some/other/dir/ - -Customising the report output ------------------------------ - -If you want to run FastQC as part of a sequencing pipeline you may wish to change the -formatting of the report to add in your own branding or to include extra information. - -In the Templates directory you will find a file called 'header_template.html' which -you can edit to change the look of the report. This file contains all of the header for -the report file, including the CSS section and you can alter this however you see fit. - -If you want to add in your own logo or other image files to the reports then you can drop -a png or jpg file into the Icons folder in the templates directory and this will be copied -into the report folder for all reports generated by the program. You can refer to these -icons using a relative URL (eg Icons/image.png) in the HTML template. Images placed -outside the icons directory will not be copied. - -Whilst you can make whatever changes you like you should probably leave in place the -
structure of the html template since later code will expect to close the main div -which is left open at the end of the header. There is no facility to change the code in -the main body of the report or the footer (although you can of course change the styling). - -The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the -report it created. You can use these placeholders in other parts of the header if you -wish. diff --git a/SequenceAnalysis/resources/external/fastqc/LICENSE b/SequenceAnalysis/resources/external/fastqc/LICENSE new file mode 100644 index 000000000..94a9ed024 --- /dev/null +++ b/SequenceAnalysis/resources/external/fastqc/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/SequenceAnalysis/resources/external/fastqc/Main.txt b/SequenceAnalysis/resources/external/fastqc/Main.txt deleted file mode 100644 index aad1ee48a..000000000 --- a/SequenceAnalysis/resources/external/fastqc/Main.txt +++ /dev/null @@ -1 +0,0 @@ -Main-Class: uk.ac.bbsrc.babraham.FastQC.FastQCApplication diff --git a/SequenceAnalysis/resources/external/fastqc/README.txt b/SequenceAnalysis/resources/external/fastqc/README.txt deleted file mode 100644 index e08d5a2f0..000000000 --- a/SequenceAnalysis/resources/external/fastqc/README.txt +++ /dev/null @@ -1,42 +0,0 @@ -FastQC - A Quality Control application for FastQ files ------------------------------------------------------- - -Most high throughput sequencers generate output in FastQ format. This -format combines the base calls for the sequence which was generated with -an encoded quality value for each base which says how confident the -sequencer was that the base call generated was correct. - -Before proceeding with the analysis of a sequence data set it is -a good idea to do some basic quality control checks on the raw data -to ensure that there are no hidden problems which might be more -difficult to detect at a later stage. - -FastQC is an application which takes a FastQ file and runs a series -of tests on it to generate a comprehensive QC report. This will -tell you if there is anything unusual about your sequence. Each -test is flagged as a pass, warning or fail depending on how far it -departs from what you'd expect from a normal large dataset with no -significant biases. It's important to stress that warnings or even -failures do not necessarily mean that there is a problem with your -data, only that it is unusual. It is possible that the biological -nature of your sample means that you would expect this particular -bias in your results. - -FastQC can be run either as an interactive graphical application -which allows you to view results for multiple files in a single -application. Alternatively you can run the program in a non -interactive way (say as part of a pipeline) which will generate -an HTML report for each file you process. - -FastQC is a cross-platform application, written in java. In theory it -should run on any platform which has a suitable java runtime environment. -Having said that we've only tested in on Windows, MacOSX 10.6 and Linux -running the Sun v1.5 and 1.6 JREs. Please let us know what happened if -you try running it on other platforms / JREs. - -If you have any comments about FastQC we would like to hear them. You -can either enter them in our bug tracking system at: - -http://www.bioinformatics.bbsrc.ac.uk/bugzilla/ - -..or send them directly to simon.andrews@bbsrc.ac.uk. diff --git a/SequenceAnalysis/resources/external/fastqc/RELEASE_NOTES.txt b/SequenceAnalysis/resources/external/fastqc/RELEASE_NOTES.txt deleted file mode 100644 index 1e41c2c81..000000000 --- a/SequenceAnalysis/resources/external/fastqc/RELEASE_NOTES.txt +++ /dev/null @@ -1,613 +0,0 @@ -RELEASE NOTES FOR FastQC V0.10.0 --------------------------------- - -The major feature of FastQC v0.10.0 is the addition of support -for fastq files generated directly by the latest version of the -illumina pipeline (Casava v1.8). In this version the pipeline -generates gzipped fastq files by default rather than using qseq -files which can then be converted to fastq. However the fastq -files generated by casava are unusual in two ways: - -1) A single sample produces a set of fastq files with a common - name, but an incrementing number at the end. - -2) Casava FastQ files contain sequences from clusters which have - failed the internal QC, and been flagged to be filtered. - -FastQC v0.10.0 introduces a Casava mode which will merge together -fastq files from the same sample group and produce a single report. -It will also exclude any flagged entries from the analysis. You -would therefore run FastQC as normal but selecting all of the -fastq files from Casava and using casava mode for your analysis. - -Casava mode is activated from the command line by adding the ---casava option to the launch command. From the interactive -application you need to select 'Casava FastQ Files' from the drop -down file selector filter options. - -If you want to analyse casava fastq files without these extra -options then you can use treat them as normal fastq files with -no problems. - -In addition to this change there have also been changes to allow -the wrapper script to work properly under windows, and a bug was -fixed which missed of the last possible Kmer from every sequence -in a library. - - -RELEASE NOTES FOR FastQC V0.9.6 -------------------------------- - -FastQC v0.9.6 fixes a couple of bugs which aren't likely to have -affected the majority of fastqc users: - -- Fixed a crash in the Kmer module when analysing a sequence where - every sequence in a library contained a poly-N stretch at its - 3' end. - -- Fixed the wrapper script so that OSX users launching fastqc - through the script rather than the Mac application bundle get - their classpath set correctly, and can therefore analyse bam/sam - files. - - -RELEASE NOTES FOR FastQC V0.9.5 -------------------------------- - -FastQC v0.9.5 fixes some bugs in the programs text output and -improves a few things in the graphical interface. Main changes -are: - -- Progress calculations are now exact and not approximate - -- The UI now has a welcome screen so you're not just presented - with a blank screen when the program starts - -- The wrapper script now sets the classpath correctly in windows - as well as linux. - -- The text report for per-base sequence content now reports - correct values for grouped bases - -- The HTML report uses a custom stylesheet for print output so - graphs aren't cut off when reports are printed. - -- Fixed a bug in testing for a warning in the per-base sequence - content module. - -- Alt text in HTML reports now matches the graphic it describes - - -RELEASE NOTES FOR FastQC V0.9.4 -------------------------------- - -FastQC v0.9.4 is a minor bugfix release which changes the offline -version of the program so that if a file fails to be processed a -full backtrace of the error is produced, rather than just a -simple generic error message. - -RELEASE NOTES FOR FastQC V0.9.3 -------------------------------- - -FastQC v0.9.3 adds support for fastq files compressed with -bzip2 in addition to its existing support for gzip compressed -files. It's worth noting that although bzip2 offers a reduction -in the file size of the compressed files (about a 5-fold size -reduction compared to raw fastq. Gzip is a 4-fold decrease), -there is a significant penalty in terms of the speed of -decompression of these files. In our tests gzipped files were -actually processed slightly faster than raw FastQ files, presumably -due to the lower amount of data transfer from disk required, -however bzip2 compressed files took around 6X as long to -process as gzipped files. - -The other big change in this release is an update to the default -CSS layout such that viewing the HTML reports doesn't require -lots of scrolling up and down the page. As before the CSS can -be edited and customised by editing the templates shipped with -the program. Many thanks to Phil Ewels who did much of the -work on the new layout. - - - -RELEASE NOTES FOR FastQC V0.9.2 -------------------------------- - -FastQC v0.9.2 fixes two bugs which were identified in the -previous release. - -1) In the text output for the per-base quality module the -correct base numbers weren't being included for files which -used grouped base ranges. - -2) The Kmer analysis module could crash when analysing very -small files, such that no position in the file had more than -1000 instances of an enriched Kmer. - -Both of these issues should now be resolved. - - -RELEASE NOTES FOR FastQC V0.9.1 -------------------------------- - -FastQC v0.9.1 adds some new command line options and fixes a -couple of usability issues. - -The new command line options are: - ---quiet Will suppress all progress messages and ensure that only -warnings or errors are written to stderr. This might be useful -for people running fastqc as part of a pipeline. - ---nogroup Will turn off the dynamic grouping of bases in the -various per-base plots. This would allow you to see a result -for each base of a 100bp run for example. This option should -not be used for really long reads (454, PacBio etc) since it -has the potential to crash the program or generate very wide -output plots - -In addition to these the following changes have been made: - -The basic stats module now includes a line to say which type -of quality encoding was found so this information isn't just -present in the header of the per-base quality plot, and will -appear in the text based output. - -We now distinguish between Illumina <1.3, 1.3 and 1.5 encodings -rather than just <1.3 and >=1.3. The Sanger encoding is now -labelled as Sanger / Illumina 1.9+ to allow for the change in -encoding in the latest illumina pipeline. - -A bug was fixed which caused the program to crash when encountering -a zero length colorspace file (which shouldn't happen anyway, but -crashing wasn't the correct response). - -The interactive over-represented sequence table now allows you -to copy out each cell individually which makes it easy to copy -any unknown sequences into other programs. - - -RELEASE NOTES FOR FastQC V0.9.0 -------------------------------- - -FastQC v0.9.0 makes a number of changes primarily targetted at -datasets containing longer reads. It allows all of the analyses -within FastQC to be completed sensibly and without excessive -resource usage on runs containing reads up to tens of kilobases -in length. - -For long reads the program now converts many of its plots to -variably sized bins so that, for example you see every base for -the first 10 bases, then every 5 bases for the next 40 bases, -then every 50, then 100 then 1kb per bin, until the end of the -sequence is reached. For sequences below 75bp the reports will -look exactly the same as before. For groups running slightly -longer Illumina or ABI runs you'll see some compression at the -end of your reads, and people using 454 or PacBio will get -sensible results for all analyses for the first time. - -One additional change which will impact anyone using reads over -75bp is that the duplicate sequence and overrepresented sequence -plots now only use the first 50bp of each read if the total read -length is over 75bp. This is because these plots work on the -basis of an exact sequence match, and longer reads tend to show -more errors at the end which makes them look like different -sequences when they're actually the same. 50bp should be enough -that you won't see exact matches by chance. - - - -RELEASE NOTES FOR FastQC V0.8.0 -------------------------------- - -FastQC v0.8.0 adds some new options for parsing BAM/SAM files and -makes the graphs in the report easier to interpret. - -All graphs in v0.8.0 now have marker lines going across them to make -it easier to relate the data in the graph to the y-axis. The per -base quality boxplots have shading behind the graph to indicate ranges -of good, medium and bad quality sequence. - -For BAM/SAM files you can now specify that you wish to analyse only -the mapped sequences in the file. This is particularly of use to -people working on colorspace data where the mapped data should -produce reliable sequence, whereas the current raw conversion to -base space may overrepresent any errors which are present. The -option to use only mapped data is set by using the - --f bam_mapped or -f sam_mapped - -option on the command line, or by specifying Mapped BAM/SAM files -from the drop down file filter in the file chooser in the interactive -version of the program. - -For FastQ files the parser has been updated to not treat blank lines -between entries or at the end of the file as a format violation since -many sequences in the public repositories can have this problem. - -From the command line we now offer the option to process multiple -files in parallel by setting the -t/--threads option. Please note that -using more than 1 thread will increase the amount of allocated memory -(250MB per thread), so you need to be sure you have enough memory (and -disk bandwidth) to be able to process more than one file. The -interactive application still defaults to a single processing thread -but you could theoretically change this by passing the correct java -properties in the startup command. - - -RELEASE NOTES FOR FastQC V0.7.2 -------------------------------- - -FastQC v0.7.2 fixes a bug in libraries where no unique sequences -were observed. It also improves the collection of duplicate -statistics on libraries with very low diversity. - -A new command line option has been added to allow the user to -manually specify a contaminant's file rather than using the sitewide -default. This would be useful if you have different sets of -contaminants to screen against for different libraries, or if you -wanted to make a custom set of contaminants, but didn't have -sufficient privileges to modify the sitewide contaminants file. - - -RELEASE NOTES FOR FastQC V0.7.1 -------------------------------- - -FastQC v0.7.1 makes some significant enhancements to the fastqc -wrapper script which make it easier to use as part of a pipeline. - -You can now use normal unix options to create your fastqc -command rather than having to pass java system properties. The -old options will continue to work though, so the updated -wrapper is still compatible with any previous commands you may -have in place. Full details of the new options can be found -by running - -fastqc --help - -One new option is the --format option which allows you to manually -specify the input format of a file, rather than having FastQC -guess the format from the file name. This would allow you to have -a BAM file called test.dat and process it using: - -fastqc --format bam test.dat - - - - -RELEASE NOTES FOR FastQC V0.7.0 -------------------------------- - -FastQC v0.7.0 introduces a new analysis module which looks at the -enrichment of short sequences within the library. It is possible -to get enrichment of unaligned subsequences to quite a high degree -without this being apparent in any of the existing modules. This -new module should find problems such as read through into the -adapters at the other end of libraries, which other analyses would -miss. - -Other changes in this release include: - -* Altering the fastqc wrapper script so it can identify when it's - being used on the source distribution of the software so it can - issue an appropriate warning. - -* Tidied up all of the y-axes on the graphs so that scaling should - now always be perfect in all graphs. - - -RELEASE NOTES FOR FastQC V0.6.1 -------------------------------- - -FastQC v0.6.1 is a bugfix release which fixes a problem with sequences -from BAM/SAM files which map to the reverse strand of the reference. - -In these cases the sequence contained in the BAM/SAM file is reverse -complemented and the qualities are reversed relative to the original -sequence which came off the sequencer. In the previous release this -meant that the plots were incorrectly showing a mix of forward and -reversed sequences. - -In v0.6.1 any sequences mapping to the reverse strand of the reference -are converted back to their original state before being analysed which -should give a clearer view of the overall qualities and sequence biases -within the run. - - -RELEASE NOTES FOR FastQC V0.6.0 -------------------------------- - -FastQC v0.6 adds support for reading SAM/BAM files as well as still -supporting fastq files. File type detection is based on the filename -so SAM/BAM files need to be named .sam or .bam. Any other form of -filename is assumed to be a fastq file. - -SAM/BAM reading was added through the use of the picard libraries, which -means that the launcher for FastQC has had to be modified to include -the picard libraries into the classpath. If you use the bat file launcher, -the wrapper script or the Mac application bundle then you won't need to -do anything to get the new version to work, but if you've created your -own launcher then you will need to modify your classpath statement to -include the sam-1.32.jar file into the classpath. - -The only other change in this release is that the line graphs have been -improved to use smoother lines for the graphs. - - - -RELEASE NOTES FOR FastQC V0.5.1 -------------------------------- - -Release 0.5.1 fixes a couple of bugs and makes some improvements to -existing functions. - -* A bug was fixed which caused the headers of the overrepresented - sequences results to not be separated in the text output. - -* A bug was fixed which caused spikes to appear in the %GC profile - when using read lengths >100bp - -* The fitting of the theoretical distribution to the %GC profile - was improved - -* Some new entries were added to the contaminants file to cover - Illumina oligos for multiplexing, tag expression and small RNA - protocols (thanks to Aaron Statham for providing these) - - -RELEASE NOTES FOR FastQC V0.5.0 -------------------------------- - -FastQC v0.4.4 makes a number of changes to the previous -release which hopefully improve the relevance of the output. - -* The fitting of the normal curve to the %GC distribution has - been improved for shorter sequences - -* Each section of the HTML report output now has a pass/warn/fail - icon next to it, rather than just having them at the top - -* The duplicate level analysis now estimates the total percentage - of sequences which are not unique, reports this on the graph and - uses this as the basis for the pass/warn/fail filtering - -* The structure of the HTML output folder has been changed so that - icons and images are put into subfolders so the only files at - the top level are ones which the user is intended to open directly. - - -RELEASE NOTES FOR FastQC V0.4.3 -------------------------------- - -FastQC v0.4.3 is a bugfix release which fixes a bug and adds -an extra check to the interactive program. - -In versions of the program since v0.2 the total sequence count -in the Basic Stats module may have been incorrect by a few percent -(either high or low). This is because instead of using the real -sequence count the module was using an estimated count which should -only be used for updating the progress indicators. The module -has now been fixed to report the actual sequence count. - -In the interactive application there was no warning given if you -chose to save a report and opted to overwrite an existing report. You -will now be warned in this case an offered the chance to use a -different filename. This change won't affect the non-interactive -mode of the program where report files will be overwritten if the -program is run more than once on the same set of data. - -RELEASE NOTES FOR FastQC V0.4.2 -------------------------------- - -FastQC v0.4.2 is a minor release which fixes some bugs and improves -the warnings on some of the analysis modules. - -Bugs which were fixed were: - -* The per-base quality plot showed an incorrect scale on the - y-axis. This was usually off by about 2, but could be more - depending on the data. The relative relationships shown - were correct, it was just the scale bar which was wrong. - -* The sequence parser incorrectly identified some base called - files as colorspace files where they contained dots in place - of N base calls. This has now been improved but will still - fail for the base where a base called file starts with an - entry which is a single called base followed by all dots - since this is indistinguishable from a colorspace fastq file. - -* Some JREs (notably OpenJDK) can't cope with a headless environment - being set from within the program. I've therefore added code - to the fastqc wrapper script to externally set the headless - environment up to bypass this problem. - -Other improvements which have been made are: - -* When writing out graphs for the HTML report we now scale some - graphs by the length of the sequences analysed so we don't get - really squashed graphs. The interactive application will still - scale the graphs to the size of the window - -* More checks have been added to the parsing of FastQ files to - ensure we're looking at the correct file format. A better reporting - mechanism has been added to allow the program to cope better with - problems during parsing. - -* The per-sequence GC plot has been modified to add in a modelled - normal distribtion over the observed distribution so you can see - how well the two fit. - -* All modules (apart from the general stats) now have valid checks - in place, and all can now produce warnings and failures. Some of - the checks in the existing modules have been changed to better cope - with libraries with very low or high GC content. - - -RELEASE NOTES FOR FastQC V0.4.1 -------------------------------- - -FastQC v0.4.1 is a bugfix release which changes the operation -of the duplicate sequence and overrepresented sequence modules. - -Both of these modules now only track sequences which appear in -the first 200,000 sequences of a file. This change was made -because people using longer read lengths found that tracking -the first million sequences led to the program exhausting its -allocated memory. - -The other change is that the duplicate sequence module now -tracks sequence counts to the end of the file rather than -stopping after a million sequences. This means the final -duplication counts seen are much more realistic and should -match with what you would see in a genome browser. Because -of this change the cutoffs to flag a file with a warning or -an error have been increased. You now get a warning when -the sum of duplicated sequences is more than 20% of the -unique sequences. You get an error when there are more -duplicated sequences than unique sequences. - - -RELEASE NOTES FOR FastQC V0.4 ------------------------------ - -FastQC v0.4 introduces a new analysis module, and easier way -to launch the program from the command line and a new output -file, as well as fixing a few minor bugs. - -The new analysis module is the sequence duplication level -module. This is a complement to the existing overrepresented -sequences module in that it looks at sequences which occur -more than once in your data. The new module takes a more -global view and says what proportion of all of your sequences -occur once, twice, three times etc. In a diverse library most -sequences should occur only once. A highly enriched library -may have some duplication, but higher levels of duplication -may indicate a problem, such as a PCR overamplification. - -In response to several requests we've also now introduced a -new output file into the report. This is a text based, tab -delimited file which includes all of the data show in the -graphs in the graphical report. This would allow people -running pipelines to store the data generated by fastQC and -analyse it systematically rather than just taking the -pass/fail/warn summary, or reviewing the reports manually. - -Finally, if you're running fastqc from the command line we've -now included a 'fastqc' wrapper script which you can launch -directly rather than having to construct a java launch -command. You can still pass -Dxxx options through to the -program, but for simple analyses you can now simply run: - -fastqc [some files] - -..once you have included the FastQC install directory into your -path. More details are in the install document. - -Other minor changes: - -- The over-represented sequences module now scans the first -million sequences to decide which sequences to track to the -end of the file. - -- The labeling on the per-base N content graph is now correct - - - -RELEASE NOTES FOR FastQC V0.3.1 -------------------------------- - -V0.3.1 is a bugfix release which fixes a few minor problems. - -1) The template system now correctly checks that it only imports -graphics files from the templates directory into the report -files and doesn't break when it encounters unexpected files. - -2) The offline mode now correctly reports the progress of all -processed files rather than just the first one. - -3) The documentation has been updated to include information on -the blue mean line in the per base quality plot. - - -RELEASE NOTES FOR FastQC V0.3 ------------------------------ - -Major new additions to v0.3 are listed below: - -1) Support for gzip compressed fastq files. You can now -load gzip compressed fastq files into FastQC in the same -way as uncompressed files. The files will be decompressed -interactively and can be viewed in the same way as for -uncompressed files. - -2) Contaminant identification. If your library is found to -have overrepresented sequences in it these are now scanned -against a database of common contaminants (primers, adapters etc) -to see if the source of the contamination can be identified. -The database is stored in a new Contaminants folder in the -main installation directory, and can be updated with your -own protocol specific sequences. - -3) When in non-interactive mode you can now pass a -preference -Dfastqc.output_dir to provide an alternative location -to save reports to, rather than having them in the same -directory as the source fastq files. - -Some improvements have also been made to the colorspace support -so this version should support a wider range of colorspace -fastq files. - - -RELEASE NOTES FOR FastQC V0.2 ------------------------------ - -There are a few new additions in v0.2 of FastQC - -1) Colorspace support: We now have rudimentary support for the -analysis of fastq files in colorspace. The analysis is done by -converting the colorspace calls to basecalls, which isn't ideal -but is hopefully more useful than nothing. - -2) Option to unzip reports. The default action in non-interactive -mode is now to both create a zip file containing the FastQC report -and to unzip this into a folder of the same name. If you just want -to generate the zip files you can add -Dfastqc.unzip=false to the -command line to suppress this new behaviour - -3) It is now possible to customise the HTML report for your site. -There is an HTML template which can be edited to add your own -branding to the reports you generate. - -4) In addition to the human readable HTML report we now also -generate a tab delimited summary file which should make it -easier to integrate FastQC into an automated reporting system -which spots any potential problems with the data. - - -RELEASE NOTES FOR FastQC V0.1.1 -------------------------------- - -This point release fixes a problem when running FastQC in a -non-interactive mode on a system without a graphical display. -The program should now operate correctly on headless systems -as long as the filename(s) to process are specified on the -command line. - - -RELEASE NOTES FOR FastQC V0.1 -------------------------------- - -FastQC v0.1 is a beta release it should work in its present state but -we are keen to get feedback on the program. In particular we are -interested to hear if anyone has: - -1) Suggestions for other checks we could be performing. - -2) Comments about the criteria we set for issuing warnings or errors and -suggestions for how these could be improved. - -You can report feedback either though our bug reporting tool at: - -www.bioinformatics.bbsrc.ac.uk/bugzilla/ - -...or directly to simon.andrews@bbsrc.ac.uk diff --git a/SequenceAnalysis/resources/external/fastqc/Templates/header_template.html b/SequenceAnalysis/resources/external/fastqc/Templates/header_template.html index bbd34b399..588d8f2f0 100644 --- a/SequenceAnalysis/resources/external/fastqc/Templates/header_template.html +++ b/SequenceAnalysis/resources/external/fastqc/Templates/header_template.html @@ -1,4 +1,3 @@ - FastQC Report @@ -7,10 +6,11 @@ - - + +

-

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788e458e3..163168b53 100644 Binary files a/SequenceAnalysis/resources/external/fastqc/uk/ac/babraham/FastQC/Utilities/QualityCount.class and b/SequenceAnalysis/resources/external/fastqc/uk/ac/babraham/FastQC/Utilities/QualityCount.class differ diff --git a/SequenceAnalysis/resources/external/jbzip2-0.9.jar b/SequenceAnalysis/resources/external/jbzip2-0.9.jar deleted file mode 100644 index 803be9d32..000000000 Binary files a/SequenceAnalysis/resources/external/jbzip2-0.9.jar and /dev/null differ diff --git a/SequenceAnalysis/resources/external/qscript/IndelRealignerRunner.scala b/SequenceAnalysis/resources/external/qscript/IndelRealignerRunner.scala deleted file mode 100644 index badb29148..000000000 --- a/SequenceAnalysis/resources/external/qscript/IndelRealignerRunner.scala +++ /dev/null @@ -1,35 +0,0 @@ -import org.broadinstitute.gatk.queue.QScript -import org.broadinstitute.gatk.queue.extensions.gatk._ - -class IndelRealignerRunner extends QScript { - - qscript => - - // Required arguments. All initialized to empty values. - @Input(doc="The reference file for the bam files.", shortName="R") - var referenceFile: File = _ // _ is scala shorthand for null - - @Input(doc="One or more bam files.", shortName="I") - var bamFiles: List[File] = Nil - - @Output(fullName = "output", shortName = "o", doc = "the output file") - var output: File = _ - - @Output(fullName = "targetIntervals", shortName = "targetIntervals", doc = "the intervals file output from RealignerTargetCreator") - var targetIntervals: File = _ - - @Argument(fullName="scatterCount", shortName="scatterCount", doc="the number of concurrent jobs", required=false) - var scatterCount: Int = 1 - - def script(){ - val realigner = new IndelRealigner - realigner.R = this.referenceFile - realigner.I = this.bamFiles - realigner.out = this.output - realigner.bam_compression = 9 - realigner.targetIntervals = this.targetIntervals - realigner.scatterCount = this.scatterCount - - add(realigner) - } -} \ No newline at end of file diff --git a/SequenceAnalysis/resources/external/sam-1.96.jar b/SequenceAnalysis/resources/external/sam-1.96.jar deleted file mode 100644 index bcb94a844..000000000 Binary files a/SequenceAnalysis/resources/external/sam-1.96.jar and /dev/null differ diff --git a/SequenceAnalysis/resources/external/tableToGraph.r b/SequenceAnalysis/resources/external/tableToGraph.r deleted file mode 100644 index c16f6a40c..000000000 --- a/SequenceAnalysis/resources/external/tableToGraph.r +++ /dev/null @@ -1,53 +0,0 @@ -library(reshape) -library(lattice) -library(plyr) -library(ggplot2) -library(grid) -library(perm) -library(gridExtra) -library(naturalsort) - -library(getopt); -library(Matrix); - -spec <- matrix(c( - 'inputFile', 'i', 1, "character", - 'outputFile', 'o', 1, "character", - 'plotTitle', 't', 2, "character", - 'xLabel', NA, 2, "character", - 'yLabel', NA, 2, "character", - 'xColIdx', NA, 1, "integer", - 'yColIdx', NA, 1, "integer", - 'hasHeaders', 'h', 2, "logical" -), ncol=4, byrow=TRUE); -opts = getopt(spec, commandArgs(trailingOnly = TRUE)); - -if ( is.null(opts$yLabel ) ) { opts$yLabel = "" } -if ( is.null(opts$xLabel ) ) { opts$xLabel = "" } -if ( is.null(opts$plotTitle ) ) { opts$plotTitle = "" } -if ( is.null(opts$hasHeaders ) ) { opts$hasHeaders = TRUE } - -df <- read.table(opts$inputFile, quote="\"", header = opts$hasHeaders); - -xColName <-names(df)[opts$xColIdx]; -yColName <- names(df)[opts$yColIdx]; -#str(df) - -P<-ggplot(df,aes_string(x=xColName,y=yColName)) + - ggtitle(opts$plotTitle) + - #scale_y_continuous(limits=c(0,2),labels=c("0.0","0.5","1.0","1.5","2.0")) + - geom_point(stat='identity') + - theme( - #axis.text.x = element_blank(), - plot.margin = unit(c(0.3,0.3,0.3,0.3),"in"), - plot.title = element_text(size=14,vjust=2), - axis.title.x = element_text(size=14,vjust=-1), - axis.title.y = element_text(size=14,vjust=2), - strip.text.x = element_text(size = 12,face="bold")) + - xlab(opts$xLabel) + - ylab(opts$yLabel) - - -png(opts$outputFile,width=880, height=680) -print(P); -dev.off(); \ No newline at end of file diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java index 8b11dea00..545d5c30f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java @@ -220,8 +220,8 @@ private String processOutput(List inputFiles, Set filesCreated, @Nul return ""; } - String output = ""; - String header = "

File Summary:

    "; + StringBuilder output = new StringBuilder(); + StringBuilder header = new StringBuilder("

    File Summary:

      "); try { @@ -233,7 +233,7 @@ private String processOutput(List inputFiles, Set filesCreated, @Nul File htmlFile = getExpectedHtmlFile(f); if (!htmlFile.exists()) { - output += "

      Unable to find output for file: " + f.getName() + "

      "; + output.append("

      Unable to find output for file: ").append(f.getName()).append("

      "); continue; } @@ -268,16 +268,16 @@ private String processOutput(List inputFiles, Set filesCreated, @Nul css = ""; html = html.replaceAll("\n", ""); - output += delim + html; + output.append(delim).append(html); delim = "
      "; //also build a header: - header += "
    • " + title + "
      • "; + header.append("
    • ").append(title).append("
      • "); //remove footer except on final file if (counter < inputFiles.size() - 1) { - output = output.replaceAll("
      .*
      ", ""); + output = new StringBuilder(output.toString().replaceAll("
      .*
      ", "")); } counter++; @@ -285,9 +285,9 @@ private String processOutput(List inputFiles, Set filesCreated, @Nul if (inputFiles.size() > 1) { - header += "

    "; + header.append("

"); String tag = "
"; - output = output.replace(tag, tag + header); + output = new StringBuilder(output.toString().replace(tag, tag + header)); } } catch (IOException e) @@ -304,7 +304,7 @@ private String processOutput(List inputFiles, Set filesCreated, @Nul } } - return output; + return output.toString(); } private String readCompressedHtmlReport(File htmlFile) throws IOException @@ -367,13 +367,17 @@ private List getBaseParams() throws FileNotFoundException File libDir = new File(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.NAME).getExplodedPath(), "lib"); File fastqcDir = new File(libDir.getParentFile(), "external/fastqc"); - File bzJar = new File(libDir, "bzip2-0.9.1.jar"); - if (!bzJar.exists()) - throw new RuntimeException("Not found: " + bzJar.getPath()); + File jbzip2 = new File(libDir, "bzip2-0.9.1.jar"); + if (!jbzip2.exists()) + { + throw new RuntimeException("Not found: " + jbzip2.getPath()); + } - File samJar = new File(libDir, "sam-1.96.jar"); - if (!samJar.exists()) - throw new RuntimeException("Not found: " + samJar.getPath()); + File htsjdkJar = new File(libDir, "htsjdk-3.0.1.jar"); + if (!htsjdkJar.exists()) + { + throw new RuntimeException("Not found: " + htsjdkJar.getPath()); + } File commonsMath = new File(libDir, "commons-math3-3.6.1.jar"); if (!commonsMath.exists()) @@ -381,12 +385,28 @@ private List getBaseParams() throws FileNotFoundException throw new RuntimeException("Not found: " + commonsMath.getPath()); } + // NOTE: the maven repo has been unreliable, but we could ultimately switch to use that: + //File jhdf5 = new File(libDir, "cisd-jhdf5-14.12.6.jar"); + File jhdf5 = new File(libDir.getParentFile(), "external/cisd-jhdf5.jar"); + if (!jhdf5.exists()) + { + throw new RuntimeException("Not found: " + jhdf5.getPath()); + } + + // NOTE: FastQC expects an alternate package name within this JAR, so use their packaged code instead: +// File base64 = new File(libDir, "base64-2.3.8.jar"); +// if (!base64.exists()) +// { +// throw new RuntimeException("Not found: " + base64.getPath()); +// } + List classPath = new ArrayList<>(); classPath.add("."); classPath.add(fastqcDir.getPath()); - classPath.add(samJar.getPath()); - classPath.add(bzJar.getPath()); + classPath.add(htsjdkJar.getPath()); + classPath.add(jbzip2.getPath()); classPath.add(commonsMath.getPath()); + classPath.add(jhdf5.getPath()); params.add("-classpath"); params.add(StringUtils.join(classPath, File.pathSeparator)); diff --git a/jbrowse/build.gradle b/jbrowse/build.gradle index 6d2eb13b3..0e19a553b 100644 --- a/jbrowse/build.gradle +++ b/jbrowse/build.gradle @@ -2,13 +2,9 @@ import org.labkey.gradle.util.BuildUtils; repositories { mavenCentral() - // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + // Added for jhdf5 from FASTQC / sequence analysis module maven { - url "https://clojars.org/repo" - } - // Added for org.clojars.chapmanb:sam (required by SequenceAnalysis) - maven { - url "https://maven.scijava.org/content/groups/public" + url "https://maven.scijava.org/content/repositories/public/" } }