diff --git a/0_generate_QC_reports_DRIVER.pl b/0_generate_QC_reports_DRIVER.pl
new file mode 100755
index 0000000..ef70fbc
--- /dev/null
+++ b/0_generate_QC_reports_DRIVER.pl
@@ -0,0 +1,24 @@
+#!/usr/bin/perl -w
+
+use strict;
+use autodie qw(:all);
+
+use File::Rsync;
+
+use Settings;
+
+my $settings = new Settings();
+
+# Generate the report
+my $command = "perl 1_download_files_and_generate_report.pl";
+system("$command");
+
+# Copy to distribution path
+my $rsync = new File::Rsync({
+    archive => 1,
+    delete => 1
+});
+$rsync->exec({
+    src => 'reports/',
+    exclude => ['_README.md'],
+    dest => $settings->{'dist_path'}}) or die("Rsync failed $!");
diff --git a/1_download_files_and_generate_report.pl b/1_download_files_and_generate_report.pl
new file mode 100755
index 0000000..3388790
--- /dev/null
+++ b/1_download_files_and_generate_report.pl
@@ -0,0 +1,88 @@
+#!/usr/bin/perl -w
+
+# Results written to working/* with the current date
+
+use strict;
+use autodie qw(:all);
+use DBI;
+use DBD::Oracle;
+use POSIX qw/strftime/;
+use POSIX::strptime qw(strptime);
+use Settings;
+use File::Copy qw(copy);
+
+# takes a string and date format
+# returns a time-tuple
+sub parse_date {
+    my ($mday, $mon, $year) = (strptime($_[0], $_[1]))[3,4,5];
+    return (0, 0, 0, $mday, $mon, $year, 0, 0, 0);
+}
+
+my $settings = new Settings();
+$ENV{ORACLE_HOME} = $settings->{'env_oracle_home'};
+my $db=DBI->connect(
+    "dbi:Oracle:host=$settings->{'host'};sid=$settings->{'sid'};port=$settings->{'port'}", 
+    $settings->{'user'},
+    $settings->{'password'},
+    {RaiseError => 1});
+
++# Get latest run date.
+my $query = "SELECT MAX(TO_DATE(L.RUNNAME, 'DD-MON-YY')) " .
+            "FROM $settings->{'schema'}.Lab_Miseq_Run L ";
+my $sth = $db->prepare($query);
+$sth->execute();
+my @lastRunInDB = parse_date($sth->fetchrow(), '%d-%b-%y');
+
+# Only report on runs we haven't done before.
+# TODO: this seems like an amaturish solution.
+my @lastRunReported = undef;
+my $timestamp = undef;
+my ($mday, $mon, $year) = undef;;
+if (-e "last_run.txt") {
+    open $timestamp, "<last_run.txt";
+    @lastRunReported = parse_date(<$timestamp>, $settings->{'date_format'});
+    close($timestamp);
+}
+if (@lastRunReported && @lastRunReported == @lastRunInDB) {
+    print "Reports up to date. Not creating a new report.\n";
+    exit 0;
+}
+
+my $fileName = strftime($settings->{'date_format'}, localtime) . ".csv";
+my $dir = "working";
+unless (-e $dir) { mkdir($dir); }
+open(my $output, ">$dir/$fileName");
+
+# Dump data to a CSV file.
+$query = "SELECT L.RUNNAME, R.*, I.* FROM $settings->{'schema'}.Lab_MiSeq_Run L " .
+         "LEFT JOIN $settings->{'schema'}.MiSeqQC_RunParameters R " .
+         "ON TO_DATE(L.RUNNAME, 'DD-MON-YYYY') = R.RUNSTARTDATE " .
+         "LEFT JOIN $settings->{'schema'}.MiSeqQC_InterOpSummary I " .
+         "ON R.RUNID = I.RUNID " .
+         "WHERE R.RUNSTARTDATE IS NULL OR R.RUNSTARTDATE >= TO_DATE('$settings->{'start_date'}', 'DD-MON-YY')";
+$sth = $db->prepare($query);
+$sth->execute();
+
+print $output join(",", @{$sth->{NAME}}) . "\n";
+while (my @row = $sth->fetchrow_array()) {
+    @row = map { defined($_)? $_ : "NA" } @row;
+    print $output join(",", @row) . "\n";
+}
+$sth->finish();
+
+# Generate report from csv, and move it to /reports, and delete the csv file
+my $sitesFolder = $settings->{'sites_path'};
+my $folderName = strftime($settings->{'date_format'}, localtime);
+my $reportFolder = "$sitesFolder/$folderName";
+unless (-e $reportFolder) { mkdir($reportFolder); }
+
+system("/usr/bin/env Rscript 2_generate_report.R $dir/$fileName $reportFolder > /dev/null 2>&1");
+rename("report.html", "$reportFolder/index.html");
+copy("R2HTML.css", "$reportFolder/R2HTML.css");
+unlink("$dir/$fileName"); # delete csv
+
+open $timestamp, ">last_run.txt";
+print $timestamp strftime($settings->{'date_format'}, @lastRunInDB);
+close($timestamp);
+
+exit;
diff --git a/2_generate_report.R b/2_generate_report.R
new file mode 100755
index 0000000..f8d4d0f
--- /dev/null
+++ b/2_generate_report.R
@@ -0,0 +1,280 @@
+#!/usr/bin/env Rscript
+
+library(R2HTML)
+library(Cairo)
+source(file="westgard.R")
+
+###############################################################################
+# Settings/constants                                                          #
+###############################################################################
+
+# Absolute paths to make this R script launchd / crontab friendly
+currPath = "./"
+scriptName = "2_generate_report.R"
+
+# Customization.
+clusterdensity.min <- 500
+clusterdensity.max <- 1200
+
+# Plot settings.
+plotWidth <- 800
+plotHeight <- 500
+plotColor <- c("black", "forestgreen")
+plotType <- "o"
+plotLwd <- 2
+plotPch <- c(16, 17)
+flagColor <- c("red", "red")
+flagPch <- c(1, 17)
+plotColumns <- 3
+plotRows <- 2
+
+# Westgard rules in use (defined in westgard.R).
+westgardRules <- c(westgard.1_3s, westgard.2_2s, westgard.4_1s, westgard.R4s, westgard.10x)
+
+###############################################################################
+# Data-related/utility functions                                              #
+###############################################################################
+
+westgard <- function (x) {
+    z <- standardize(x)
+    Reduce("|", lapply(westgardRules, function (rule) rule(z)))
+}
+
+# Format a number for display in a table.
+table.format <- function (n) {
+    formatC(n, format="f", digits=2)
+}
+
+# Scale down outliers which are more than dev.max standard deviations
+# away from the mean.
+shrink.outliers <- function(x, dev.max) {
+    xmean <- mean(x)
+    xsd <- sd(x)
+    xmin <- xmean - dev.max*xsd
+    xmax <- xmean + dev.max*xsd
+    x[x < xmin] <- xmin
+    x[x > xmax] <- xmax
+    x
+}
+
+
+###############################################################################
+# Plotting-related functions                                                  #
+###############################################################################
+
+# Add circles to indicate points have been flagged.
+flag.points <- function (x, y, flags, pch, col) {
+    points(x[flags], y[flags], pch=pch, cex=2, lwd=2, col=col)
+}
+
+# Add reference lines for different standard deviation values
+lines.mean.sd <- function (y) {
+    my.mean <- mean(y)
+    my.sd <- sd(y)
+    abline(h=my.mean, lwd=2)
+    abline(h=my.mean + my.sd, lty="dotted", lwd=2, col="green3")
+    abline(h=my.mean - my.sd, lty="dotted", lwd=2, col="green3")
+    abline(h=my.mean + 2*my.sd, lty="longdash", lwd=2, col="darkgoldenrod1")
+    abline(h=my.mean - 2*my.sd, lty="longdash", lwd=2, col="darkgoldenrod1")
+    abline(h=my.mean + 3*my.sd, lwd=2, col="red")
+    abline(h=my.mean - 3*my.sd, lwd=2, col="red")
+}
+
+###############################################################################
+# HTML-related functions                                                      #
+###############################################################################
+
+# Make an HTML image map for a scatterplot.
+make.image.map <- function (x, y, titles, map.name) {
+    x.dev <- as.integer(grconvertX(x, to="device"))
+    y.dev <- as.integer(grconvertY(y, to="device"))
+
+    html <- c(paste0('<map name="', map.name, '">'))
+    areas <- apply(cbind(x.dev, y.dev, titles), 1, function (row) {
+        sprintf('<area shape="circle" coords="%s,%s,5" title="%s" nohref>', 
+                row[1], row[2], row[3])
+    })
+    html <- c(html, areas)
+    c(html, "</map>")
+}
+
+# Make an HTML list of items
+make.html.list <- function (items) {
+    c("<ul>", paste0("<li>", items, "</li>"), "</ul>")
+}
+
+###############################################################################
+# Read and process data                                                       #
+###############################################################################
+
+# Read the CSV file (dump of MiSeqQC_RunParameters JOIN MiSeqQC_InteropSummary).
+args<-commandArgs(TRUE)
+if (length(args) != 2) { stop(paste("Syntax: ./", scriptName, " <csvFile> <outpath>", sep="")) }
+filePath <- args[1]
+fileName <- gsub(".csv", "", basename(filePath))
+reportDir <- args[2]
+data <- read.csv(filePath, header=TRUE)
+
+# Read list of parameters (name,desc,unit).
+param.list <- read.csv("parameter_list.csv", header=T, stringsAsFactors=F)
+rownames(param.list) <- param.list$parameter
+param.list$ylab <- with(param.list, 
+                        ifelse(!is.na(param.unit),
+                               paste0(param.desc, " (", param.unit, ")"), 
+                               param.desc))
+
+# Read list of reagents (name,desc).
+reagent.list <- read.csv("reagent_list.csv", header=T, stringsAsFactors=F)
+rownames(reagent.list) <- reagent.list$reagent
+
+# Parse dates.
+data$RUNSTARTDATE <- as.Date(data$RUNSTARTDATE, "%d-%b-%y")
+expiration.cols <- paste0(reagent.list$reagent, "_EXPIRATION")
+data[,expiration.cols] <- lapply(data[,expiration.cols], as.Date, format="%d-%b-%y")
+data <- data[order(data$RUNSTARTDATE),]
+
+# Collect missing runs, and remove from further analysis.
+missing.runs <- data[is.na(data$RUNID.1),]
+data <- data[!is.na(data$RUNID.1),]
+
+# Change proportions to percentages.
+data$Q30_1 <- data$Q30_1*100
+data$Q30_2 <- data$Q30_2*100
+
+# Apply Westgard rules.
+flags <- apply(data[,param.list$parameter], 2, westgard)
+colnames(flags) <- paste0(colnames(flags), ".FLAG")
+data <- cbind(data, flags)
+
+# Number of days until expiration dates.
+reagent.cols <- paste0(reagent.list$reagent, "_EXPIRATION")
+days.left <- lapply(data[,reagent.cols], function(col) as.numeric(col-Sys.Date()))
+names(days.left) <- sub("_EXPIRATION", ".DAYSLEFT", names(days.left))
+data <- cbind(data, days.left)
+
+# Create alerts.
+# Runs missing from QC tables.
+alerts <- apply(missing.runs, 1, function (row) {
+    sprintf("Sample sheet created on %s has no associated QC data", row["RUNNAME"],
+            strftime(row["RUNSTARTDATE"], "%b %d, %Y"))
+})
+# Parameters flagged on most recent run.
+flag.cols <- colnames(data)[grepl("[.]FLAG$", colnames(data))]
+most.recent <- data[nrow(data), flag.cols]
+most.recent <- most.recent[,which(t(most.recent))]
+alerts <- c(alerts, sapply(names(most.recent), function (col) {
+    sprintf("Parameter %s has been flagged",
+            sub(".FLAG", "", col, fixed=T))
+}))
+# Reagents which are about to expire or have already expired.
+expire.cols <- colnames(data)[grepl("[.]DAYSLEFT$", colnames(data))]
+most.recent <- data[nrow(data), expire.cols]
+most.recent <- most.recent[,which(t(most.recent) < 31)]
+alerts <- c(alerts, sapply(names(most.recent), function (col) {
+    sprintf("The %s will expire in %d days",
+            sub(".DAYSLEFT", "", col, fixed=T),
+            most.recent[,col])
+}))
+
+###############################################################################
+# Make plots                                                                  #
+###############################################################################
+
+x <- data$RUNSTARTDATE
+xlab <- "run date"
+point.labels <- strftime(data$RUNSTARTDATE, "%b %d, %Y")
+
+nup <- plotRows*plotColumns
+nplots <- as.integer(nrow(param.list)/(nup))+1
+. <- sapply(seq(0, nplots-1), function (i) {
+    params <- param.list[(i*nup+1):(i*nup+nup),"parameter"]
+    params <- params[!is.na(params)]
+    plotName <- paste0("parameters", i, ".png")
+    CairoPNG(file.path(reportDir, plotName), width=plotWidth, height=plotHeight)
+    par(yaxs="i", mfrow=c(plotRows, plotColumns), mar=c(2, 2, 1, 1), oma=c(1, 1, 0, 4))
+    sapply(1:length(params), function (i) {
+        y <- data[,params[i]]
+        flag <- data[,paste0(params[i], ".FLAG")]
+        ylim <- c(mean(y)-4*sd(y), mean(y)+4*sd(y))
+        y.scaled <- shrink.outliers(y, 4)
+        title <- param.list[params[i],"ylab"]
+        plot(x, y.scaled, ylim=ylim, type="n")
+        lines.mean.sd(y)
+        points(x, y.scaled, type=plotType, pch=plotPch[1], col=plotColor[1], lwd=plotLwd,
+                 xlab=NA, ylab=NA, ylim=ylim)
+        flag.points(x, y.scaled, flag, flagPch[1], flagColor[1])
+        if (i %% plotColumns == 0 | i == length(params)) {
+            axis(4, at=mean(y)+sd(y)*seq(-3, 3), labels=seq(-3, 3))
+        }
+        
+        limits <- par("usr")
+        xmiddle <- (limits[1] + limits[2])/2
+        ymax <- limits[4]
+        text(xmiddle, ymax, title, font=2, cex=1.5, pos=1)
+    })
+    mtext("standard deviations from mean", side=4, outer=T, line=2)
+    dev.off()
+})
+
+image.maps <- c()
+
+# Report 1: Cluster Density
+CairoPNG(file.path(reportDir, "REPORT-1.png"), 
+    width=plotWidth, height=plotHeight, bg="transparent")
+y <- data$CLUSTERDENSITY
+ymin <- min(c(clusterdensity.min, y))
+ymax <- max(c(clusterdensity.max, y))
+plot(x, y, type=plotType, pch=plotPch[1], col=plotColor[1], lwd=plotLwd,
+     ylim=c(ymin, ymax), xlab=xlab, ylab=param.list["CLUSTERDENSITY","ylab"])
+
+flag <- data$CLUSTERDENSITY.FLAG
+flag.points(x, y, flag, flagPch[1], flagColor[1])
+flag <- y > clusterdensity.max | y < clusterdensity.min
+flag.points(x, y, flag, flagPch[2], flagColor[2])
+
+abline(h=clusterdensity.min, lty="longdash", lwd=3)
+abline(h=clusterdensity.max, lty="longdash", lwd=3)
+text(max(x), clusterdensity.min, labels=clusterdensity.min, pos=3, cex=1.5)
+text(max(x), clusterdensity.max, labels=clusterdensity.max, pos=3, cex=1.5)
+
+title(main="Cluster density")
+grid(nx=0, ny=NULL, col="black")
+legend(par("usr")[2], par("usr")[4], xjust=1, yjust=0, xpd=T,
+       legend=c("Tolerance", "Flagged (Westgard)", "Flagged (outside tolerance)"),
+       lty=c("longdash", NA, NA), pch=c(NA, flagPch), col=c("black", flagColor))
+image.maps <- c(image.maps, make.image.map(x, y, point.labels, "REPORT1Map"))
+dev.off()
+
+
+# Report 2: % bases passing Q30 cutoff
+CairoPNG(file.path(reportDir, "REPORT-2.png"), 
+    width=plotWidth, height=plotHeight, bg="transparent")
+par(yaxs="i")
+q30.means <- c(mean(data$Q30_1), mean(data$Q30_2))
+q30.stdevs <- c(sd(data$Q30_1), sd(data$Q30_2))
+ymin <- min(q30.means-4*q30.stdevs)
+ymax <- max(c(q30.means+4*q30.stdevs, 100))
+
+y <- data$Q30_1
+flag <- data$Q30_1.FLAG
+plot(x, y, type=plotType, col=plotColor[1], lwd=plotLwd, pch=plotPch[1],
+     ylim=c(ymin, ymax), ylab="bases passing Q30 cutoff (%)", xlab=xlab)
+flag.points(x, y, flag, flagPch[1], flagColor[1])
+
+y <- data$Q30_2
+flag <- data$Q30_2.FLAG
+lines(x, y, type=plotType, pch=plotPch[2], col=plotColor[2], lwd=plotLwd)
+flag.points(x, y, flag, flagPch[1], flagColor[1])
+
+title(main="Bases passing Q30 cutoffs")
+grid(nx=0, ny=NULL, col="black")
+legend(par("usr")[2], par("usr")[4], xjust=1, yjust=0, xpd=T,
+       legend=c("read 1", "read 2", "Flagged (Westgard)"), 
+       col=c(plotColor, flagColor[1]), pch=c(plotPch, flagPch[1]))
+image.maps <- c(image.maps, make.image.map(c(x, x), c(data$Q30_1, data$Q30_2), 
+                                           c(point.labels, point.labels), 
+                                           "REPORT2Map"))
+dev.off()
+
+# Finally, generate the report.
+Sweave("report.Rnw", driver=RweaveHTML, syntax="SweaveSyntaxNoweb")
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..92ebae6
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,192 @@
+Setting up a developer workstation
+==================================
+
+This will document the installation steps to get the MiSeq QC reports running
+locally on your workstation.
+
+The steps are for Eclipse with EPIC on Ubuntu, adapt as needed to your preferred
+IDE or operating system.
+
+1. Check the version of Java you have installed:
+
+        java -version
+ 
+2. If the java version is lower than 1.7, then install JDK7:
+
+        sudo apt-get install openjdk-7-source
+
+3. Check what version of perl you have installed. These reports were tested
+   with version 5.18.2, but earlier versions may also work.
+
+        perl -v
+
+4. If it's not there, install it.
+
+        sudo apt-get install perl
+
+5. Install Eclipse, although you might prefer a more recent version from the
+   [Eclipse web site][eclipse]:
+
+        sudo apt-get install eclipse
+
+   [eclipse]: https://www.eclipse.org/downloads/
+
+6. Launch Eclipse. From the Help menu, choose either Eclipse Marketplace... or 
+   Install New Software....
+
+7. In the marketplace, just type EPIC and search. In the install wizard, use
+   the [EPIC update site][epic].
+   [epic]: http://e-p-i-c.sf.net/updates/
+
+7. From the Window menu, choose Preferences, and navigate down to Perl EPIC:
+   Editor.
+   * Use spaces instead of tabs.
+   * Insert 4 spaces on indent.
+   * Show line numbers (your choice)
+   * Show print margin (your choice)
+
+8. From the File menu, choose Import.... Navigate down to Git: Projects from Git.
+
+9. Choose Clone URI, and paste this URI: 
+   https://github.com/cfe-lab/MiSeqQCReport.git
+
+10. Ask your supervisor for the password, and use the defaults for everything 
+    else. Select the new project wizard with a Perl project.
+
+11. Change the folder to point at the new miseq_qc_report folder created by git,
+    and finish the import.
+
+12. Install [Oracle Instant Client][oracle]. Use the basic lite version, and 
+    test that sqlplus works. You will probably have to follow the steps to set 
+    up the libraries, and you may have to run sqlplus64 instead of sqlplus.
+
+        sqlplus USER@\"//192.168.?.?:1521/SID\"
+
+    If you want to have history and tab expansion in sqlplus, install rlwrap:
+
+        sudo apt-get install rlwrap
+        alias sqlplus="rlwrap sqlplus"
+
+    You also need to set the `ORACLE_HOME` environment variable.
+
+        sudo vi /etc/profile.d/oracle.sh # Add the following line:
+        export ORACLE_HOME=/usr/lib/oracle/12.1/client64
+
+    [oracle]: https://help.ubuntu.com/community/Oracle%20Instant%20Client
+
+13. Install Perl's Database Interface package (DBI), File::Rsync, and XML::Simple.
+
+        sudo apt-get install libdbi-perl libfile-rsync-perl libxml-simple-perl
+
+14. Install DBD::Oracle CPAN module. The first command will begin the 
+    installation of CPAN, just accept the defaults. It will eventually open a
+    `cpan>` prompt where you can enter the second command. That eventually
+    opens a root shell where you can enter the rest.
+
+        sudo cpan
+        look DBD::Oracle
+        . /etc/profile.d/oracle.sh
+        perl Makefile.PL
+        make
+        make test # Won't be able to connect to database, that's fine.
+        make install
+        exit
+        exit
+
+    If you encounter the error  "Unable to locate an oracle.mk or other
+    suitable *.mk", replace "perl Makefile.PL" with "perl Makefile.PL
+    -l".
+
+14. Repeat the above commands, without the oracle.sh part, for the
+    packages IPC::System::Simple, File::Rsync, and POSIX::strptime.
+
+14. Copy the `QC_Reports/Settings_template.pm` file, and modify the settings to
+    match your environment.
+
+14. Install the Cairo development library.
+        
+        sudo apt-get install libcairo2-dev
+
+15. Install R. The last two commands are run in the R console, and you should
+    check the [StatET installation page][statet] to see exactly which version
+    of the rj package is compatible with the version of StatET you are going to
+    install. You also need to install the R2HTML and Cairo packages.
+
+        sudo apt-get install r-base r-base-dev
+        sudo R
+        install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")
+        install.packages("R2HTML")
+        install.packages("Cairo")
+        q()
+
+    [statet]: http://www.walware.de/it/statet/installation.mframe
+
+16. Launch Eclipse. For some reason, you can't currently install StatET from the
+    Eclipse Marketplace, so from the Help menu, choose Install New Software....
+
+17. Go to the [StatET installation page][statet], and find the update site for
+    your version of Eclipse. Paste that address in the install wizard, and 
+    select the StatET for R component. Finish the installation.
+
+18. From the Window menu, choose Preferences. Navigate down to StatET: 
+    Run/Debug: R Environments.
+
+19. Click the Add... button.
+
+20. Next to the Location (R_HOME) field, press the + button, and choose Try
+    find automatically. It should find the R you just installed.
+
+21. Click the Detect Default Properties/Settings button. Click OK. Click OK.
+
+22. If you want an R console, open the Run menu, and choose 
+    Run Configurations.... Select R Console and click the add button. Click Run.
+
+23. To run an R script with command-line arguments, modify the R console 
+    configuration by setting the working directory and adding this to the 
+    Options/Arguments field with whatever CSV file name was created by the
+    previous step:
+    
+        --args working/2014-06-25.csv
+    
+    Then you can use `source("2_generate_report.R")` in the console to launch it.
+
+24. If you get an error about a missing font -adobe-helvetica-...,
+    install the gsfonts-x11 package and refresh your font cache.
+
+        sudo apt-get install gsfonts-x11
+        xset fp rehash
+
+The reports are currently run on a virtual machine by a certain user,
+and then displayed on the local network. They are scheduled under that
+virtual machine's user's crontab at 8:00 AM each day. You can see the
+tasks by logging in as that user and then typing `crontab -l`. For the
+IP addresses of the machine, and the user as whom you must log on, ask
+your supervisor.
+
+
+Setting up Oracle
+=================
+
+To run the scripts, you will need access to certain Oracle tables.
+
+1. Ask the database administrator to create an account for you, with
+   read access to the MiSeqQC_* tables. This will need to be okayed by
+   the lab director. You will be told the default password. Also ask for
+   the IP address, port, and SID for the Oracle database.
+
+2. The account will be created with a default password. Log in for the
+   first time, and change the password.
+
+        sqlplus username/password@//dbhost:1521/SID
+
+   You will be prompted to enter a new password. Oracle passwords at the
+   CfE must conform to the following guidelines:
+       * Password can not be same as username
+       * Password must be different than previous 3 passwords
+       * Password must be at least 8 characters long
+       * Password must begin with letter (all letters in uppercase)
+       * Password must contain at least two digits
+       * Password must contain at least one punctuation !"#$%&()*+,-/:;<=>?_
+   If you have chosen a password which fulfills all these criteria, but
+   get errors about an invalid login, contact the database administrator
+   and ask to set your password on her computer.
diff --git a/R2HTML.css b/R2HTML.css
new file mode 100644
index 0000000..d9f6002
--- /dev/null
+++ b/R2HTML.css
@@ -0,0 +1,59 @@
+html, body {
+    width: 800;
+    margin: auto;
+}
+
+h1, h2 {
+    font-family: sans-serif;
+}
+
+img {
+    margin: auto;
+    padding: 0px;
+}
+
+table, th, td {
+    border: 1px solid grey;
+}
+
+th, td {
+    padding: 5px;
+}
+
+table {
+    width: 100%;
+    border-collapse: collapse;
+}
+
+.image_cell {
+    margin: auto;
+    text-align: center;
+}
+
+.number_cell {
+    text-align: right;
+}
+
+area {
+    cursor: pointer;
+    display: block;
+}
+
+dt {
+    font-family: sans-serif;
+    font-weight: bold;
+}
+
+dt:not(.noclear) {
+    float: left;
+    clear: left;
+    margin-right: 5px;
+}
+
+dt:after {
+    content: ":";
+}
+
+dd {
+    padding: 0 0 0.5em 0;
+}
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..40037c4
--- /dev/null
+++ b/README.md
@@ -0,0 +1,75 @@
+How to Change QC Report Parameters
+==================================
+
+Settings for this project are stored in two files:
+  - database-related settings are in Settings.pm
+  - report-related settings are in the top of 2_generate_report.R
+
+
+Changing the run start date
+---------------------------
+Open "Settings.pm" in a text editor. Look for these lines near the
+bottom of the file.
+
+        # When to start counting from.
+        start_date => "01-NOV-13"
+
+Here, "01-NOV-13" is the start date (it may be a different date in the
+file). Change that to the start date you want to use, but keep the
+formatting of the date the same. For example, to change the start date
+to January 31, 2014, I would edit the lines to look like this.
+
+        # When to start counting from.
+        start_date => "31-JAN-14"
+
+
+Changing the Westgard rules
+---------------------------
+Edit "2_generate_report.R", and look for the variable "westgardRules" in
+the top section. The available rules are defined in the file
+"westgard.R". As of this writing, all the "common" rules (taken from the
+website http://www.westgard.com/mltirule.htm) were defined. Put the
+functions for whichever rules you want to use in this array.
+
+Next, edit "report.Rnw", which is an html file with some R code chunks,
+to describe the new Westgard rules you are using. The relevant part is
+in a <small> tag near the bottom of the body (search for Westgard).
+
+
+Changing the cluster density tolerances
+---------------------------------------
+Edit "2_generate_report.R", and look for the variables
+"clusterdensity.min" and "clusterdensity.max" in the top section. Edit
+these to whatever values you like. The changes will be automatically
+shown in the report (you do not need to edit "report.Rnw").
+
+
+Developer notes
+===============
+
+If you are not a programmer, you do not need to read this section.
+
+Database information
+--------------------
+
+The MiSeq QC report primarily uses information from two Oracle tables.
+- MISEQQC_RUNPARAMETERS contains the reagent expration dates.
+- MISEQQC_INTEROPSUMMARY contains the run parameters (CLUSTERDENSITY
+  etc.)
+These two tables are linked by the RUNID field. In theory, there should
+be one row of MISEQQC_INTEROPSUMMARY for each row in
+MISEQQC_RUNPARAMETERS, but this is not currently the case. These tables
+get populated after a run is complete and Eric's Interop parsing scripts
+run. Evidently, there is something wrong with the scripts.
+
+Additionally, the LAB_MISEQ_RUN table has an entry for each run. It is
+populated whenever anybody creates a new sample sheet in the QAI. Again,
+there be a one-to-one relationship between LAB_MISEQ_RUN.RUNNAME
+and MISEQQC_RUNPARAMETERS.EXPERIMENNAME (and by extension
+MISEQQC_INTEROPSUMMARY.RUNID). However, the MISEQQC* tables get
+populated by scripts after the run has completed, so it's possible that
+runs don't appear there if the scripts break. 
+
+Also, if a run is aborted, then it will be in the LAB_MISEQ_RUN table
+but not in the MISEQQC* tables. Currently, it is not recorded anywhere
+if a run was aborted or not.
diff --git a/Settings_template.pm b/Settings_template.pm
new file mode 100644
index 0000000..09a8fc5
--- /dev/null
+++ b/Settings_template.pm
@@ -0,0 +1,37 @@
+# Copy this file to Settings.pm, then edit all the configuration entries to
+# match your environment.
+
+package Settings;
+
+sub new {
+    my ($class_name) = @_;
+    my ($self) = {
+        # Database client
+        env_oracle_home => "/usr/oracle_instantClient64",
+        
+        # Database connection params
+        host => "192.168.?.?",
+        port => "1521",
+        sid => "??????",
+        user => "??????",
+        password => "??????",
+        schema => "??????",
+        
+        # This is an rsync path.
+        dist_path => "dist",
+        
+    	# Where to put reports.
+    	sites_path => "reports",
+
+        # Date format for file names. To the day in prod, to the minute in dev.
+        date_format => "%Y-%m-%d_%H%M",
+
+        # When to start counting from.
+        start_date => "01-NOV-13"
+    };
+    
+    bless ($self, $class_name);
+    return $self;
+}
+
+1;
diff --git a/dist/_README.md b/dist/_README.md
new file mode 100644
index 0000000..241a807
--- /dev/null
+++ b/dist/_README.md
@@ -0,0 +1,2 @@
+This folder is a dummy target for rsync in development. In production, rsync
+will send the files to the public web server.
diff --git a/parameter_list.csv b/parameter_list.csv
new file mode 100644
index 0000000..3238b80
--- /dev/null
+++ b/parameter_list.csv
@@ -0,0 +1,29 @@
+parameter,param.desc,param.unit
+ALIGNED_F,"reads aligned, forward",%
+ALIGNED_R,"reads aligned, reverse",%
+Q30_1,"bases passing Q30, read 1",%
+Q30_2,"bases passing Q30, read 2",%
+CLUSTERDENSITY,cluster density,1000/mm^2
+PERCENTCLUSTERSPF,clusters passing filters,%
+PHASING_F,"phasing, forward",%
+PHASING_R,"phasing, reverse",%
+PREPHASING_F,"prephasing, forward",%
+PREPHASING_R,"prephasing, reverse",%
+ERRORRATE_F,"error rate, forward",%
+ERRORRATE_R,"error rate, reverse",%
+INT_1_1_A,"A intensity, read 1, cycle 1",NA
+INT_1_1_C,"C intensity, read 1, cycle 1",NA
+INT_1_1_G,"G intensity, read 1, cycle 1",NA
+INT_1_1_T,"T intensity, read 1, cycle 1",NA
+INT_1_20_A,"A intensity, read 1, cycle 20",NA
+INT_1_20_C,"C intensity, read 1, cycle 20",NA
+INT_1_20_G,"G intensity, read 1, cycle 20",NA
+INT_1_20_T,"T intensity, read 1, cycle 20",NA
+INT_2_1_A,"A intensity, read 2, cycle 1",NA
+INT_2_1_C,"C intensity, read 2, cycle 1",NA
+INT_2_1_G,"G intensity, read 2, cycle 1",NA
+INT_2_1_T,"T intensity, read 2, cycle 1",NA
+INT_2_20_A,"A intensity, read 2, cycle 20",NA
+INT_2_20_C,"C intensity, read 2, cycle 20",NA
+INT_2_20_G,"G intensity, read 2, cycle 20",NA
+INT_2_20_T,"T intensity, read 2, cycle 20",NA
diff --git a/reagent_list.csv b/reagent_list.csv
new file mode 100644
index 0000000..b7f9f70
--- /dev/null
+++ b/reagent_list.csv
@@ -0,0 +1,4 @@
+reagent,description
+FLOWCELL,flow cell
+PR2,PR2 incorporation buffer
+REAGENTKIT,reagent kit
diff --git a/report.Rnw b/report.Rnw
new file mode 100644
index 0000000..4a29591
--- /dev/null
+++ b/report.Rnw
@@ -0,0 +1,116 @@
+<html>
+<head>
+    <title>
+        MiSeq QC Report for \Sexpr{strftime(Sys.Date(), format="%B %d, %Y")}
+    </title>
+    <script type="text/javascript">
+        /* Get the next element sibling. */
+        function nextElement(n) {
+            x = n.nextSibling;
+            while (x.nodeType != 1) {
+                x = x.nextSibling;
+            }
+            return x;
+        }
+
+        /* Display and hide images by clicking table rows. */
+        function toggleImage(row){
+            ncol = row.querySelectorAll("td").length;
+            graph_cell = nextElement(row).querySelector("td");
+            graph_cell.setAttribute("colspan", ncol);
+            if (graph_cell.style.display == "none") {
+                graph_cell.style.display = "table-cell";
+            } else {
+                graph_cell.style.display = "none";
+            }
+        }
+    </script>
+</head>
+
+<body>
+    <h1>MiSeq QC Report for \Sexpr{strftime(Sys.Date(),, format="%B %d, %Y")}</h1>
+
+    <dl>
+        <dt>Run ID</dt>
+        <dd>\Sexpr{data[nrow(data), "RUNID"]}</dd>
+        <dt>Run Date</dt>
+        <dd>\Sexpr{strftime(data[nrow(data), "RUNSTARTDATE"], "%B %d, %Y")}</dd>
+        <dt>Cutoff Date</dt>
+        <dd>\Sexpr{strftime(min(data$RUNSTARTDATE), "%B %d, %Y")}</dd>
+<<echo=F, results=html>>=
+    html <- c(apply(reagent.list, 1, function (row) {
+        daysleft <- data[nrow(data), paste0(row["reagent"], ".DAYSLEFT")]
+        desc <- paste0("<dt>Days until ", row["description"], " expiration</dt>")
+        item <- paste0("<dd>", daysleft, "</dd>")
+        c(desc, item)
+    }))
+    paste0(html, collapse="\n")
+@
+    </dl>
+
+    <h2>Alerts</h2>
+<<echo=F, results=html>>=
+    if (length(alerts) > 0) {
+        paste0(make.html.list(alerts), collapse="\n")
+    } else {
+        "<p>Nothing to report.</p>"
+    }
+@
+    <h2>Reports</h2>
+
+    <img src="REPORT-1.png" usemap="#REPORT1Map" />
+    <br />
+    <img src="REPORT-2.png" usemap="#REPORT2Map" />
+    <br />
+
+    <h2>Parameters</h2>
+    <p>Values more than 4 standard deviations away from the mean are shown at 4 standard deviations.</p>
+<<echo=F, results=html>>=
+    html <- sapply(0:(nplots-1), function (i) {
+        paste0('<img src="parameters', i, '.png" /><br />')
+    })
+    paste0(html, collapse="\n")
+@
+    <table>
+        <thead>
+            <tr>
+               <th>Parameter</th>
+               <th>Description</th>
+               <th>Mean</th>
+               <th>Median</th>
+               <th>Standard Deviation</th>
+            </tr>
+        </thead>
+        <tbody>
+<<echo=F, results=html>>=
+    tbody <- c(sapply(param.list$parameter, function (p) {
+        cells <- c(paste0('<td class="text_cell">', p, "</td>"))
+        cells <- c(cells, paste0('<td class="text_cell">', param.list[p, "param.desc"], "</td>"))
+        cells <- c(cells, paste0('<td class="number_cell">', table.format(mean(data[,p])), "</td>"))
+        cells <- c(cells, paste0('<td class="number_cell">', table.format(median(data[,p])), "</td>"))
+        cells <- c(cells, paste0('<td class="number_cell">', table.format(sd(data[,p])), "</td>"))
+        c('<tr>', cells, "</tr>")
+    }))
+    paste0(tbody, collaspe="\n")
+@
+        </tbody>
+    </table>
+    <br/>
+
+    <small>
+    <p>Using the following Westgard rules: 1<sub>3s</sub> (one measurement
+    &gt;3&sigma; away from the mean), 2<sub>2s</sub> (two consecutive
+    measurements &gt;2&sigma; in the same direction), 4<sub>1s</sub> (four
+    consecutive measurements &gt;1&sigma; in the same direction),
+    R4s (change from &gt;2&sigma; to &lt;2&sigma; or vice versa), 10x
+    (ten or more consecutive measurements on one side of the mean).</p>
+    
+    <p>Using tolerances of \Sexpr{clusterdensity.min} and
+    \Sexpr{clusterdensity.max} to flag cluster density.</p>
+    </small>
+
+<<echo=F, results=html>>=
+    paste0(image.maps, collapse="\n")
+@
+</body>
+</html>
diff --git a/reports/_README.md b/reports/_README.md
new file mode 100644
index 0000000..2f36327
--- /dev/null
+++ b/reports/_README.md
@@ -0,0 +1 @@
+This folder holds the reports that get generated.
\ No newline at end of file
diff --git a/westgard.R b/westgard.R
new file mode 100644
index 0000000..38a3503
--- /dev/null
+++ b/westgard.R
@@ -0,0 +1,53 @@
+# http://www.westgard.com/mltirule.htm
+standardize <- function (x) {
+    (x-mean(x))/sd(x)
+}
+
+# x is a boolean vector
+# replace all runs of TRUE in x which are shorter than minlen with FALSE
+conseq.trues <- function (x, minlen) {
+    r <- rle(x)
+    r$values <- r$values & r$lengths >= minlen
+    inverse.rle(r)
+}
+
+# In each of the rule functions, z is assumed to be standardized,
+# that is, z is a vector of standard deviations away from the mean.
+
+westgard.1_3s <- function (z) {
+    abs(z) > 3
+}
+
+westgard.1_2s <- function (z) {
+    abs(z) > 2
+}
+
+westgard.2_2s <- function (z) {
+    conseq.trues(z > 2, 2) | conseq.trues(z < -2, 2)
+}
+
+westgard.R4s <- function (z) {
+    d <- abs(diff(z)) > 4
+    s <- diff(sign(z)) > 0
+    conseq.trues((c(d, F) | c(F, d)) & (c(F, s) | c(s, F)) & abs(z) > 2, 2)
+}
+
+westgard.3_1s <- function (z) {
+    conseq.trues(z > 2, 3) | conseq.trues(z < -2, 3)
+}
+
+westgard.4_1s <- function (z) {
+    conseq.trues(z > 2, 4) | conseq.trues(z < -2, 4)
+}
+
+westgard.8x <- function (z) {
+    conseq.trues(z > 0, 8) | conseq.trues(z < 0, 8)
+}
+
+westgard.10x <- function (z) {
+    conseq.trues(z > 0, 10) | conseq.trues(z < 0, 10)
+}
+
+westgard.12x <- function (z) {
+    conseq.trues(z > 0, 12) | conseq.trues(z < 0, 12)
+}
diff --git a/working/_README.md b/working/_README.md
new file mode 100644
index 0000000..a521525
--- /dev/null
+++ b/working/_README.md
@@ -0,0 +1 @@
+This folder holds working files that are used to prepare a report. 
\ No newline at end of file