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sisyphus.pl
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#!/usr/bin/perl -w
use FindBin; # Find the script location
use lib "$FindBin::Bin/lib";# Add the script libdir to libs
use strict;
use POSIX ":sys_wait_h";
use Getopt::Long;
use Pod::Usage;
use File::Basename;
use Cwd qw(abs_path);
use Molmed::Sisyphus::Common;
=pod
=head1 NAME
sisyphus.pl - Watch a runfolder and start processing it when it is completed
=head1 SYNOPSIS
sisyphus.pl -help|-man
sisyphus.pl -runfolder <runfolder> [-debug -noexec]
=head1 OPTIONS
=over 4
=item -h|-help
prints out a brief help text.
=item -m|-man
Opens the manpage.
=item -runfolder
The runfolder to process.
=item -noexec
Do not execute the generated batchscript
=item -nowait
Skip paranoid wait for runfolder completion. Just continue if RTAComplete.txt exists.
=item -force
Continue even if data is missing. Adds --ignore-missing-stats, --ignore-missing-bcl, --ignore-missing-control to bcl2fastq conversion.
=item -miseq
Also upload the entire MiSeq runfolder to a subfolder in the runfolder on Uppmax
=item -ignoreQCResult
Proceed with the data processing, even though one or multiple QC criteria have failed.
=item -noPostProcessing
Will not upload any data to UPPMAX nor start any post processing jobs (neither on UPPMAX nor locally).
=item -localPostProcessing
Will not upload any data to UPPMAX or start any jobs on UPPMAX. Will run the post processing jobs
locally instead, and upload the data directly to Swestore.
=item -noSeqStatSync
Sync data to ngi-pipeline host
=item -debug
Print debugging information
=back
The rest of the configuration is read from RUNFOLDER/sisyphus.yml. See example included in the sisyphus directory.
=head1 DESCRIPTION
Sisyphus.pl waits for completion of a runfolder and then generates and executes a shell script
for post processing the data.
The postprocessing includes the following steps:
=over 4
=item Conversion from bcl to fastq, including demultiplexing
=item Extraction of summary data to a separate folder
=item Transfer of selected files to UPPMAX
=item Fastq statistics collection
=item Extraction of projects for data delivery
=item Archiving
=back
=cut
my $rfPath = undef;
my $miseq = 0;
my $exec = 1;
my $wait = 1;
my $ignoreQCResult = 0;
my $noPostProcessing = 0;
my $localPostProcessing = 0;
my $noSeqStatSync = 0;
my $ngi = 0;
my $force = 0;
our $debug = 0;
my $threads = `cat /proc/cpuinfo |grep "^processor"|wc -l`;
$threads = ($threads == 1) ? 1 : int($threads/2);
my ($help,$man) = (0,0);
GetOptions('help|?'=>\$help,
'man'=>\$man,
'runfolder=s' => \$rfPath,
'miseq!' => \$miseq,
'exec!' => \$exec,
'wait!' => \$wait,
'ignoreQCResult!' => \$ignoreQCResult,
'noPostProcessing!' => \$noPostProcessing,
'localPostProcessing!' => \$localPostProcessing,
'noSeqStatSync!' => \$noSeqStatSync,
'force!' => \$force,
'debug' => \$debug,
'j=i' => \$threads,
) or pod2usage(-verbose => 0);
pod2usage(-verbose => 1) if ($help);
pod2usage(-verbose => 2) if ($man);
unless(defined $rfPath && -e $rfPath){
print STDERR "Runfolder not specified or does not exist\n";
pod2usage(-verbose => 1);
exit;
}
# Pass debug to scripts with this flag
my $debugFlag='';
if($debug){
$debugFlag = '-debug';
}
my $sisyphus = Molmed::Sisyphus::Common->new(PATH=>$rfPath, DEBUG=>$debug);
$rfPath = $sisyphus->PATH;
my $rfName = basename($rfPath);
my $rfRoot = dirname($rfPath);
# Set defaults
my $rHost = "milou-b.uppmax.uu.se";
my $uProj = "a2009002";
my $ngiProj = "a2014205";
my $rPath = "/proj/$uProj/private/nobackup/runfolders";
my $ngiRemPath = "/proj/$ngiProj/archive";
my $oPath = "/proj/$uProj/private/nobackup/OUTBOX";
my $aHost = "milou-b.uppmax.uu.se";
my $ngiRemHost = "nestor.uppmax.uu.se";
my $aPath = "/proj/$uProj/private/";
my $sHost = "localhost";
my $sPath = dirname($rfPath) . '/summaries';
my $anPath = $rfRoot . '/MiSeqAnalysis';
my $fastqPath = undef;
my $mismatches = '1:1:1:1:1:1:1:1';
my $localProcessingPath = "/data/scratch/Local_Processing/";
my $localArchivePath = "/data/scratch/Local_Archive/";
my $irodsPath = "/ssUppnexZone/proj/a2009002/";
my $mailTo = "medsci-molmed-bioinfo\@googlegroups.com";
my $mailFrom = "seq\@medsci.uu.se";
# Read the sisyphus configuration and override the defaults
my $config = $sisyphus->readConfig();
# Setup scratch/fastq directory
if(defined $config->{FASTQ_PATH}){
$fastqPath = "$config->{FASTQ_PATH}/$rfName";
$sisyphus->mkpath($fastqPath);
if($sisyphus->df($fastqPath) < 300e9 ){
die "Too little space on fastq device $fastqPath";
}
}elsif(-d "/data/scratch" && $sisyphus->df("/data/scratch") > 300e9){
$fastqPath = "/data/scratch/$rfName";
$sisyphus->mkpath($fastqPath);
}else{
$fastqPath = "$rfPath";
}
# Only allow the -miseq flag if this is a miseq run
unless (!$miseq || $sisyphus->machineType() eq 'miseq') {
print STDERR "The -miseq flag can only be used for MiSeq run folders ('$rfPath' does not appear to be one)\n";
pod2usage(-verbose => 1);
exit;
}
# Get extra library path from config and save to a separate file
`touch $FindBin::Bin/PERL5LIB`;
if(defined $config->{PERL5LIB}){
open(my $LIB, ">$FindBin::Bin/PERL5LIB") or die "Failed to write $FindBin::Bin/PERL5LIB: $!";
foreach my $libPath (@{$config->{PERL5LIB}}){
print $LIB "$libPath\n";
}
close($LIB);
}
# Set paths from config
if(defined $config->{REMOTE_HOST}){
$rHost = $config->{REMOTE_HOST};
}
if(defined $config->{NGI_HOST}){
$ngiRemHost = $config->{NGI_HOST};
}
if(defined $config->{REMOTE_PATH}){
$rPath = $config->{REMOTE_PATH};
}
if(defined $config->{NGI_REMOTE_PATH}){
$ngiRemPath = $config->{NGI_REMOTE_PATH};
}
if(defined $config->{OUTBOX_PATH}){
$oPath = $config->{OUTBOX_PATH};
}
if(defined $config->{ARCHIVE_HOST}){
$aHost = $config->{ARCHIVE_HOST};
}
if(defined $config->{ARCHIVE_PATH}){
$aPath = $config->{ARCHIVE_PATH};
}
if(defined $config->{SUMMARY_HOST}){
$sHost = $config->{SUMMARY_HOST};
}
if(defined $config->{SUMMARY_PATH}){
$sPath = $config->{SUMMARY_PATH};
}
if(defined $config->{UPPNEX_PROJECT}){
$uProj = $config->{UPPNEX_PROJECT};
}
if(defined $config->{ANALYSIS_PATH}){
$anPath = abs_path($rfPath . '/' . $config->{ANALYSIS_PATH});
}
if(defined($config->{NGI_PROCESSING})) {
$ngi = $config->{NGI_PROCESSING};
}
if(defined($config->{LOCAL_PROCESSING})) {
$localProcessingPath = $config->{LOCAL_PROCESSING_PATH};
$localArchivePath = $config->{LOCAL_ARCHIVE_PATH};
}
unless(defined $irodsPath){
if(defined $config->{SWESTORE_PATH}){
$irodsPath = $config->{SWESTORE_PATH};
}else{
print STDERR "iRODS path must be specified\n";
pod2usage(-verbose => 1);
exit;
}
}
if (defined $config->{MAIL}) {
$mailTo = $config->{MAIL};
}
if (defined $config->{SENDER}) {
$mailFrom = $config->{SENDER};
}
# Strip trailing slashes from paths
$rPath =~ s:/*$::;
$ngiRemPath =~ s:/*$::;
$oPath =~ s:/*$::;
$aPath =~ s:/*$::;
$sPath =~ s:/*$::;
if($miseq){
$anPath =~ s:/*$::;
}
# Set combined paths
my $targetPath = "$rHost:$rPath";
my $ngiTargetPath = "$ngiRemHost:$ngiRemPath";
my $summaryPath = "$sHost:$sPath";
my $archivePath = "$aHost:$aPath";
my $rBin = "$rPath/$rfName/Sisyphus";
my $analysisPath = undef;
if($miseq){
my $analysisPath = "$anPath/$rfName";
}
if($debug){
print "\$rHost => $rHost\n";
print "\$rPath => $rPath\n";
print "\$sHost => $sHost\n";
print "\$sPath => $sPath\n";
print "\$aHost => $aHost\n";
print "\$aPath => $aPath\n";
print "\$oPath => $oPath\n";
print "\$rfName => $rfName\n";
print "\$anPath => $anPath\n";
print "\$localProcessingPath => $localProcessingPath\n";
print "\$localArchivePath => $localArchivePath\n";
};
print STDERR "All set. Checking for runfolder completion!\n\n";
my $complete = 0;
until($complete||$force){
$complete = $sisyphus->complete();
unless($complete){
print STDERR "Not complete. Going to sleep\n" if $debug;
sleep 600;
print STDERR "Trying again\n" if $debug;
}
}
if($complete){
print STDERR "Runfolder complete, checking for SampleSheet.csv\n";
}elsif($force){
print STDERR "Runfolder NOT complete, continue anyway!\n";
}
$complete = 0;
until($complete){
if(-e "$rfPath/SampleSheet.csv"){
# Check sanity of sample sheet
$complete = $sisyphus->fixSampleSheet("$rfPath/SampleSheet.csv");
print STDERR "SampleSheet has errors. Please fix it. You do not have to abort!\nJust fix the file and the script will continue after sleeping 10 minutes from now.\n" unless($complete);
}else{
print STDERR "SampleSheet.csv is missing\n";
$complete=0;
}
unless($complete) {
print STDERR "Sleeping for 10 minutes\n";
sleep 600;
}
}
# Check that the MiSeq analysis folder has finished copying, wait until it finishes otherwise
if ($miseq) {
print STDERR "Checking MiSeq Analysis folder for completion!\n\n";
$complete = 0;
until($complete) {
if (! -e $analysisPath || ! -d $analysisPath) {
print STDERR "Analysis folder does not exist, expects $analysisPath\n";
}
elsif (! -e "$analysisPath/TransferComplete.txt") {
print STDERR "Indication that transfer of analysis results is complete is missing\n";
}
else {
$complete = 1;
}
unless($complete) {
print STDERR "Sleeping for 10 minutes\n";
sleep 600;
}
}
}
die unless($complete);
print STDERR "Runfolder $rfPath ready to go!\n";
# Sleep 30 minutes as an additional precaution
sleep 1800 if($wait);
my $runInfo = $sisyphus->getRunInfo() || die "Failed to read RunInfo.xml from $rfPath\n";
# This (or rather the object method) will need changing when we have an example of a dual-index run
my $readMask = $sisyphus->createReadMask() || die "Failed to generate readMask";
my $posFormat = $sisyphus->positionsFormat();
my $machineType = $sisyphus->machineType();
# Identify tiles with too high error for exclusion
my $excludedTiles = $sisyphus->excludeTiles();
my @incTiles;
my @excTiles;
foreach my $lane (1..$sisyphus->laneCount){
if(exists $excludedTiles->{$lane}){
my $flowcellLayot = $runInfo->{xml}->{Run}->{FlowcellLayout};
if(scalar(keys %{$excludedTiles->{$lane}}) == $runInfo->{tiles} + 2 ){ # There are two extra keys in the excludedTiles hash
# Exclude the whole lane
push @excTiles, "s_${lane}";
# And also add it to lanes that should not be delivered
$sisyphus->excludeLane($lane);
}else{
for(my $surf=1; $surf<=$flowcellLayot->{SurfaceCount}; $surf++){
for(my $swath=1; $swath<=$flowcellLayot->{SwathCount}; $swath++){
for(my $t=1; $t<=$flowcellLayot->{TileCount}; $t++){
my $tile = sprintf("$surf$swath%02d", $t);
if(exists $excludedTiles->{$lane}->{$tile}){
push @excTiles, "s_${lane}_$tile";
}else{
push @incTiles, "s_${lane}_$tile";
}
}
}
}
}
}else{
push @incTiles, "s_$lane";
}
}
my $includeTiles = join ',', @incTiles;
my $ignore = '';
if($force){
$ignore = '--ignore-missing-stats --ignore-missing-bcl --ignore-missing-control ';
}
# Create processing shellscript
open(my $scriptFh, '>', "$rfPath/sisyphus.sh") or die "Failed to create '$rfPath/sisyphus.sh':$!\n";
print $scriptFh <<EOF;
#!/bin/bash
# Setup some basic mechanisms for more defensive bash scripting.
set -o pipefail
set -o nounset
PATH="$FindBin::Bin:$config->{CASAVA}:\$PATH"
check_errs()
{
# Function. Parameter 1 is the return code
# Para. 2 is text to display on failure.
# Kill all child processes before exit.
if [ "\${1}" -ne "0" ]; then
EOF
if($localProcessing) {
print $scriptFh <<EOF;
mailStatus "Processing step FAILED" "A processing step failed with the following ERROR # : \${1} : \${2}"
EOF
}
print $scriptFh <<EOF;
echo "ERROR # \${1} : \${2}"
killJobs \${1}
fi
}
killJobs() {
for job in `jobs -p`; do
kill -9 \$job
done
exit \${1}
}
mailStatus() {
# Parameter 1 is subject
# Parameter 2 is message body
echo -n "Sending status email to $mailTo ..."
$FindBin::Bin/mailStatus.pl $mailFrom $mailTo $1 $2
RETVAL = \$?
if [[ \${RETVAL} -ne 0 ]]; then
echo "Couldn't mail successfully."
killJobs \${RETVAL}
fi
}
main() {
# Get Sisyphus version
echo -n "Sisyphus version: "
if [ -e "$FindBin::Bin/.git" ]; then
git --git-dir $FindBin::Bin/.git describe --tags
elif [ -e "$FindBin::Bin/SISYPHUS_VERSION" ]; then
cat "$FindBin::Bin/SISYPHUS_VERSION"
else
echo "unknown"
fi
# Run demultiplexing
cd $rfPath
check_errs \$? "Failed to cd to $rfPath"
echo "Setting up demultiplexing"
EOF
# Configure the per lane allowed barcode mismatch
if(exists $config->{MISMATCH}){
my @mismatches = split /:/, $mismatches; # Init array with defaults
foreach my $lane (keys %{$config->{MISMATCH}}){
$mismatches[$lane-1]=$config->{MISMATCH}->{$lane};
}
$mismatches = join ':', @mismatches;
}
if ($machineType eq "hiseqx") {
$includeTiles =~ s/,/ --tiles /g;
if (-e "$fastqPath/Unaligned") {
print STDERR "\n\nERROR: $fastqPath/Unaligned already exists\n\n";
exit 1;
} else {
mkdir "$fastqPath/Unaligned";
}
print $scriptFh <<EOF;
if [ ! -e "$rfPath/Unaligned" ]; then
ln -s "$fastqPath/Unaligned" "$rfPath/Unaligned"
fi
$config->{BCL2FASTQ} -v 2>&1 | awk '{if(/^bcl2fastq/){print \$2}}' > $rfPath/bcl2fastq.version
echo "Demultiplexing/Converting to FastQ"
$config->{BCL2FASTQ} --input-dir '$rfPath/Data/Intensities/BaseCalls' --output-dir '$fastqPath/Unaligned' --use-bases-mask '$readMask' --barcode-mismatches '$mismatches' ${ignore} --tiles $includeTiles &> BclToFastq.log
check_errs \$? "bcl2fastq failed in $fastqPath/Unaligned"
EOF
if(@excTiles > 0){
my $excludeTiles = join ',', @excTiles;
if (-e "$fastqPath/Excluded") {
print STDERR "\n\nERROR: $fastqPath/Excluded already exists\n\n";
exit 1;
} else {
mkdir "$fastqPath/Excluded" unless -e "$fastqPath/Excluded";
}
print $scriptFh <<EOF;
echo "Setting up demultiplexing of excluded tiles"
EOF
$excludeTiles =~ s/,/ --tiles /g;
print $scriptFh <<EOF;
$config->{BCL2FASTQ} --input-dir '$rfPath/Data/Intensities/BaseCalls' --output-dir '$fastqPath/Excluded' --use-bases-mask '$readMask' --barcode-mismatches '$mismatches' ${ignore} --tiles --tiles $excludeTiles &> $rfPath/setupBclToFastqExcluded.err
if [ ! -e "$rfPath/Excluded" ]; then
ln -s "$fastqPath/Excluded" "$rfPath/Excluded"
fi
EOF
}
} else {
print $scriptFh <<EOF;
if [ ! -e "$rfPath/Unaligned" ]; then
ln -s "$fastqPath/Unaligned" "$rfPath/Unaligned"
fi
EOF
print $scriptFh <<EOF;
configureBclToFastq.pl --input-dir '$rfPath/Data/Intensities/BaseCalls' --output-dir '$fastqPath/Unaligned' --sample-sheet '$rfPath/SampleSheet.csv' --use-bases-mask '$readMask' --mismatches '$mismatches' ${ignore} --positions-format $posFormat --fastq-cluster-count 0 --tiles $includeTiles &> $rfPath/setupBclToFastq.err
check_errs \$? "configureBclToFastq.pl failed"
EOF
if(@excTiles > 0){
my $excludeTiles = join ',', @excTiles;
print $scriptFh <<EOF;
echo "Setting up demultiplexing of excluded tiles"
configureBclToFastq.pl --input-dir '$rfPath/Data/Intensities/BaseCalls' --output-dir '$fastqPath/Excluded' --sample-sheet '$rfPath/SampleSheet.csv' --use-bases-mask '$readMask' --mismatches 1 --positions-format $posFormat --fastq-cluster-count 0 --tiles $excludeTiles &> $rfPath/setupBclToFastqExcluded.err
check_errs \$? "configureBclToFastq.pl for excluded tiles failed"
check_errs \$? "bclt2fastq failed in $fastqPath/Excluded"
if [ ! -e "$rfPath/Excluded" ]; then
ln -s "$fastqPath/Excluded" "$rfPath/Excluded"
fi
EOF
}
print $scriptFh <<EOF;
echo "Demultiplexing/Converting to FastQ"
cd '$fastqPath/Unaligned'
check_errs \$? "Failed to cd to $fastqPath/Unaligned"
make -j$threads &> BclToFastq.log
check_errs \$? "make failed in $fastqPath/Unaligned"
EOF
if(@excTiles > 0){
print $scriptFh <<EOF;
echo "Demultiplexing/Converting excluded tiles to FastQ"
cd '$fastqPath/Excluded'
check_errs \$? "Failed to cd to $fastqPath/Excluded"
make -j$threads &> BclToFastq.log
check_errs \$? "make failed in $fastqPath/Excluded"
if [ ! -e "$rfPath/Excluded" ]; then
ln -s "$fastqPath/Excluded" "$rfPath/Excluded"
fi
EOF
}
}
# Random string used for rsync dry-run.
my $rnd = time() . '.' . rand(1);
print $scriptFh <<EOF;
# Copy $FindBin::Bin/ directory to the runfolder
# Both for archiving and usage at UPPMAX or locally
if [ -e $rfPath/Sisyphus ]; then
rm -rf $rfPath/Sisyphus
fi
echo -n "Copy $FindBin::Bin/ $rfPath/Sisyphus "
cp -a $FindBin::Bin/ $rfPath/Sisyphus/
check_errs \$? "FAILED"
echo OK
# Save the sisyphus version
if [ -e "$rfPath/Sisyphus/.git" ]; then
git --git-dir "$rfPath/Sisyphus/.git" describe --tags > "$rfPath/Sisyphus/SISYPHUS_VERSION"
check_errs \$? "Failed to get sisyphus version from $rfPath/Sisyphus/.git"
fi
EOF
# If uploading a MiSeq Analysis folder, tarball it and move it into the normal runfolder
if ($miseq) {
print $scriptFh <<EOF;
processMiSeqAnalysisFolder "$rfPath" "$rfName" "$anPath" "$analysisPath";
EOF
}
# Make the quick report
if (defined $config->{MAIL}) {
print $scriptFh <<EOF;
echo Generating quick report for $mailTo
quickReport.pl -runfolder $rfPath -mail $mailTo -sender $mailFrom
#Check if quick report could be generated.
check_errs \$? "Could not generate quickReport"
qcValidateRun.pl -runfolder $rfPath -mail $mailTo -sender $mailFrom
EOF
unless($ignoreQCResult) {
print $scriptFh <<EOF;
check_errs \$? "FAILED QC"
EOF
}
}
unless($noPostProcessing || $localPostProcessing) {
print $scriptFh <<EOF;
#Transfer data to remote host
transferFilesToRemoteHost "$rfRoot" "$rfName" "rsync.log" "rsync-real.log" "$targetPath" "hiseq.rsync"
#Calculate MD5 sum for transferred files
createMD5SumFromLogFile "$rfName" "$rfPath" "$rfRoot" "rsync.log" "checksums.md5"
#Copy calculated MD5sum to remote host
copyFolderToRemoteTarget "$targetPath" "$rfPath/MD5" "$rfName"
#Set permission on remote host
setRemotePermission "$rHost" "$rPath" "$rfName"
EOF
}
## TODO: Investigate whether or not this should be skipped or calculated for us.
unless($noSeqStatSync) {
print $scriptFh <<EOF;
rsyncSeqSummaries "$rfRoot" "$rfName" "$summaryPath" "rsync.summary.log" "summary.rsync"
EOF
}
unless($noPostProcessing) {
# The rest of the processing is done at UPPMAX or locally
unless($localPostProcessing) {
print $scriptFh <<EOF;
#Start cluster jobs on remote host
startClusterJobs "$rfRoot" "$rHost" "$rPath" "$rfName" "$debugFlag"
EOF
} else {
my $numLanes = $sisyphus->laneCount();
my $localRfPath = $localProcessingPath . '/' . $rfName;
my $localSampleSheet = $sisyphus->readSampleSheet();
my $localOPath = "$localRfPath/Projects";
$localOPath =~ s:/*$::;
my $skipLanes = [];
my $skip = "";
if(defined $config->{SKIP_LANES}){
$skipLanes = $config->{SKIP_LANES};
}
foreach my $lane (@{$skipLanes}) {
$skip .= " -skip $lane";
}
my $projs = join "\\n", keys %{$localSampleSheet};
# Add year and month to outdir and irods path if not already included
unless($localArchivePath =~ m/201\d-[0123]\d$/){
if($sisyphus->RUNFOLDER =~ m/(1\d)([01]\d)[0123]\d_/){
$localArchivePath .= "/20$1-$2";
}
}
unless($irodsPath =~ m/201\d-[0123]\d$/){
if($sisyphus->RUNFOLDER =~ m/(1\d)([01]\d)[0123]\d_/){
$irodsPath .= "/20$1-$2";
}
}
print $scriptFh <<EOF;
# Start processing jobs on local host
mailStatus "Local jobs started for $rfName" "Will now start to run fastqStats, extractProject and generateReport for $rfName."
echo -n "Creating local processing folder... "
mkdir -p $localProcessingPath
check_errs \$? "FAILED to create folder $localProcessingPath"
cd $rfRoot
check_errs \$? "Failed to cd to $rfRoot"
# Now do the actual transfer, and remove the source files afterwards.
rm -f $rfName/rsync-real.log
echo -n "rsync $rfName $localRfPath "
rsync -vrktp --remove-source-files --chmod=Dg+sx,ug+w,o-rwx --prune-empty-dirs --include-from "$FindBin::Bin/hiseq.rsync" "$rfName" "$localProcessingPath" >> "$localRfPath/rsync-real.log"
check_errs \$? "FAILED to rsync $rfName $localRfPath"
echo OK
# Enable this if we want to remove the empty directories after the transfer.
#find $pwd -depth -type d -empty -delete
#Calculate MD5 sum for transferred files
createMD5SumFromLogFile "$rfName" "$localRfPath" "$localProcessingPath" "rsync-real.log" "checksums.md5"
echo -n "Starting fastqStats.pl for all lanes in parallel... "
seq $numLanes | xargs -n 1 -P 0 -I __laneNr__ $FindBin::Bin/fastqStats.pl -runfolder $localRfPath -lane __laneNr__ $debugFlag
check_errs \$? "FAILED to run fastqStats.pl in $localRfPath"
echo OK
echo -n "Starting extractProject.pl for all projects in parallel... "
echo -e "$projs" | xargs -n 1 -P 0 -I __proj__ $FindBin::Bin/extractProject.pl -runfolder $localRfPath -project __proj__ -outdir $localOPath/__proj__ $skip $debugFlag
check_errs \$? "FAILED to run extractProject.pl in $localRfPath"
echo OK
echo -n "Starting generateReport.pl for a global report... "
$FindBin::Bin/generateReport.pl -runfolder $localRfPath $debugFlag
check_errs \$? "FAILED to run generateReport.pl in $localRfPath"
echo OK
mailStatus "Uploading data to Swestore for $rfName" "Local processing for $rfName successful. Will now create an archivable copy of the data and upload it to Swestore."
# Start uploading data directly to Swestore
echo -n "Starting to create archive of the runfolder... "
$FindBin::Bin/archive.pl -runfolder $localRfPath -outdir $localArchivePath $debugFlag
check_errs \$? "FAILED to run archive.pl in $localRfPath, outputing to $localArchivePath"
echo OK
echo -n "Starting to upload archive to Swestore... "
$FindBin::Bin/archive2swestore.pl -runfolder $localArchivePath/$rfName -config $localRfPath/sisyphus.yml -noSlurm $debugFlag
check_errs \$? "FAILED to run archive2swestore.pl in $localArchivePath/$rName"
echo OK
mailStatus "Verifying uploaded data for $rfName" "Will now start to verify that the data for $rfName was successfully uploaded to Swestore."
START_OK=1
SLEEP=300
# TODO: Måste verifieras att detta funkar bra.
until [ \$START_OK = 0 ]; do
echo -n "Verifying that data was correctly uploaded to Swestore... "
$FindBin::Bin/irods/ssverify.sh $localArchivePath/$rfName $irodsPath/test-johanhe/foo/$rfName
START_OK=\$?
if [ \$START_OK -gt 0 ]; then
echo "FAILED will retry in \$SLEEP seconds"
sleep \$SLEEP
fi
done
check_errs \$START_OK "FAILED to run ssverify.sh on $localArchivePath/$rfName and $irodsPath/$rfName"
echo OK
#echo -n "Starting archive2swetore.pl for verifying uploaded copy to Swestore... "
#$FindBin::Bin/archive2swestore.pl -runfolder $aPath -config $rfPath/sisyphus.yml -verifyonly $debugFlag
#check_errs \$? "FAILED"
#echo OK
mailStatus "Ready to deliver $rfName" "All local processing and data archivation to Swestore is now finished for $rfName. It is now ready to be delivered."
EOF
} # closes the localProcessing {
} # closes the noUppmax {
if($ngi && !$localPostProcessing) {
unless(-e "$rfPath/Demultiplexing") {
print $scriptFh <<EOF;
# Create Demultiplexing softlink
cd $rfPath
check_errs \$? "Failed to cd to $rfPath"
ln -s Unaligned Demultiplexing
#Transfer data to remote host
transferFilesToRemoteHost "$rfRoot" "$rfName" "rsync.ngi.log" "rsync-real.ngi.log" "$ngiTargetPath" "ngi.rsync"
#Calculate MD5 sum for transferred files
createMD5SumFromLogFile "$rfName" "$rfPath" "$rfRoot" "rsync.ngi.log" "checksums.ngi.md5"
#Copy calculated MD5sum to remote host
copyFolderToRemoteTarget "$ngiTargetPath" "$rfPath/MD5/checksums.ngi.md5" "$rfName"
#Set permission on remote host
setRemotePermission "$ngiRemHost" "$ngiRemPath" "$rfName"
EOF
}
#} # End bracket for main function
########################################################################
# Helper functions
########################################################################
print $scriptFh <<EOF;
processMiSeqAnalysisFolder() {
runfolderPath="";
runfolderName="";
miseqAnPath="";
miseqAnalysisPath="";
if [ -z "\$1" ]
then
echo "-runfolder path #1 is zero length or empty."
exit 1;
else
runfolderPath=\$1;
fi
if [ -z "\$2" ]
then
echo "-runfolder name #2 is zero length or empty."
exit 1;
else
runfolderName=\$2;
fi
if [ -z "\$3" ]
then
echo "-miseqAnPath #3 is zero length or empty."
exit 1;
else
miseqAnPath=\$3;
fi
if [ -z "\$4" ]
then
echo "-miseqAnalysisPath #4 is zero length or empty."
exit 1;
else
miseqAnalysisPath=\$4;
fi
if [ ! -e "\$runfolderPath/MD5" ]; then
mkdir -m 2770 \$runfolderPath/MD5
check_errs \$? "Failed to mkdir \$runfolderPath/MD5"
fi
cd \$miseqAnPath
check_errs \$? "Failed to cd to \$miseqAnPath"
if [ -e "\$runfolderName" ]; then
echo -n "Checksumming files from \$miseqAnalysisPath"
# List the contents of the MiSeq analysis folder, and calculate MD5 checksums
find '\$runfolderName' -type f | $FindBin::Bin/md5sum.pl \$runfolderName > \$runfolderPath/MD5/checksums.miseqrunfolder.md5
check_errs \$? "FAILED"
echo OK
# Tarball the entire MiSeq analysis folder and move it under the runfolder
echo -n "Tarballing MiSeq analysis folder '\$miseqAnalysisPath'"
$FindBin::Bin/gzipFolder.pl '\$runfolderName' '\$runfolderPath/MD5/checksums.miseqrunfolder.md5'
check_errs \$? "FAILED"
echo OK
echo -n "Move MiSeq analysis tarball to '\$runfolderPath'"
mv "\$runfolderName.tar.gz" "\$runfolderPath/MiSeq_Runfolder.tar.gz"
check_errs \$? "FAILED"
echo OK
# If the analysis runfolder does not exist but the tarball does, it's ok, we are just re-running the script
elif [ -e "\$runfolderPath/MiSeq_Runfolder.tar.gz" ]; then
echo -n "MiSeq analysis folder is missing, but the tarball exists. Everything is OK!"
# Else, the folders and arguments need to be verified
else
check_errs 1 "Was expecting a MiSeq analysis runfolder: '\$miseqAnalysisPath', but did not find one"
fi
}
startClusterJobs() {
runfolderRoot="";
remoteHost="";
remotePath="";
runfolderName="";
debugFlag="";
if [ -z "\$1" ]
then
echo "-runfolder root #1 is zero length or empty."
exit 1;
else
runfolderRoot=\$1;
fi
if [ -z "\$2" ]
then
echo "-remote host #2 is zero length or empty."
exit 1;
else
remoteHost=\$2;
fi
if [ -z "\$3" ]
then
echo "-remote path #3 is zero length or empty."
exit 1;
else
remotePath=\$3;
fi
if [ -z "\$4" ]
then
echo "-runfolder name #4 is zero length or empty."
exit 1;
else
runfolderName=\$4;
fi
if ! [ -z "\$5" ]
then
debugFlag=\$5;
fi
cd \$runfolderRoot
check_errs \$? "Failed to cd to \$runfolderRoot"
# Only start calculating the fastq-stats and leave the report and extraction part
# to manual start after inspection
START_OK=1
SLEEP=300
until [ \$START_OK = 0 ]; do
echo -n "Starting processing at UPPMAX "
ssh \$remoteHost "cd \$remotePath/\$runfolderName; ./Sisyphus/aeacus-stats.pl -runfolder \$remotePath/\$runfolderName \$debugFlag";
START_OK=\$?
if [ \$START_OK -gt 0 ]; then
echo "FAILED will retry in \$SLEEP seconds"
sleep \$SLEEP
fi
done
check_errs \$START_OK "FAILED"
echo OK
check_errs $? "FAILED to start aeacus-stats.pl in \$remotePath/\$runfolderName at \$remoteHost";
cd \$runfolderRoot
check_errs \$? "Failed to cd to \$runfolderRoot"
# Start extracting projects and archive data
# to manual start after inspection
START_OK=1
SLEEP=300
sleep 10
until [ \$START_OK = 0 ]; do
echo -n "Starting extracting and archiving at UPPMAX "
ssh \$remoteHost "cd \$remotePath/\$runfolderName; ./Sisyphus/aeacus-reports.pl -runfolder \$remotePath/\$runfolderName \$debugFlag";
START_OK=\$?
if [ \$START_OK -gt 0 ]; then
echo "FAILED will retry in \$SLEEP seconds"
sleep \$SLEEP
fi
done
check_errs \$START_OK "FAILED"
echo OK
check_errs \$? "FAILED to start aeacus-reports.pl in \$remotePath/\$runfolderName at \$remoteHost";
}
rsyncSeqSummaries () {
runfolderRoot="":