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fix bug: run the EDGE through command line with absoulte path

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chienchi committed Feb 23, 2016
1 parent 387f714 commit 64a9618b76a15764021b420f49c34de635c80611
Showing with 9 additions and 9 deletions.
  1. +9 −9 runPipeline
@@ -304,7 +304,7 @@ sub runUnmappedContigToRefSeq
my $file=shift;
my $db="$RealBin/database/bwa_index/NCBI-Bacteria-Virus.fna";
my $time=time();
my $outputDir="$outDir/ReferenceBasedAnalysis/UnmappedContigs";
my $outputDir="$abs_outDir/ReferenceBasedAnalysis/UnmappedContigs";
my $prefix="UnmappedContigs";
my $log="$outputDir/log.txt";
if ( -s "$outputDir/UnmappedContigs.ctg_class.csv" )
@@ -365,9 +365,9 @@ sub Contigs_taxonomyAssignment
my $file=shift;
my $db="$RealBin/database/bwa_index/NCBI-Bacteria-Virus.fna";
my $time=time();
my $outputDir="$outDir/AssemblyBasedAnalysis/Taxonomy";
my $outputDir="$abs_outDir/AssemblyBasedAnalysis/Taxonomy";
my $prefix="$project_name";
my $cov_table="$outDir/AssemblyBasedAnalysis/readsMappingToContig/readsToContigs_coverage.table";
my $cov_table="$abs_outDir/AssemblyBasedAnalysis/readsMappingToContig/readsToContigs_coverage.table";
my $tax_assignments_result="$outputDir/$prefix.ctg_class.csv";
my $log="$outputDir/log.txt";
if ($noColorLog)
@@ -466,7 +466,7 @@ sub check_reference_genome
my $referenceGenome_r = shift;
my $time=time();
my %format;
my $outputDir = "$outDir/Reference/";
my $outputDir = "$abs_outDir/Reference/";
my $referenceGenome = "$outputDir/reference.fasta";
my $referenceGBK = "$outputDir/reference.gbk";
my $gff3File="$outputDir/reference.gff";
@@ -1820,7 +1820,7 @@ sub runReadsToContig
&executeCommand($command);
&executeCommand("awk \'{print \$1\"\\t\"\$4}\' $outputDir/readsToContigs_coverage.table > $outputDir/magnitudes.txt");
&executeCommand("mv $outputDir/Final_contigs.fasta $contigFile");
chdir "$outDir/AssemblyBasedAnalysis/";
chdir "$abs_outDir/AssemblyBasedAnalysis/";
&executeCommand("perl $RealBin/scripts/contig_stats.pl -p $contigFile > contigs_stats.txt");
chdir $workingDir;
&printRunTime($time);
@@ -1877,7 +1877,7 @@ sub runContigToGenome
my $contigFile = shift;
my $referenceFile = shift;
my $time=time();
my $outputDir= "$outDir/AssemblyBasedAnalysis/contigMappingToRef";
my $outputDir= "$abs_outDir/AssemblyBasedAnalysis/contigMappingToRef";
my $outPrefix = "$outputDir/contigsToRef";
my $identity_cutoff = $configuration->{identity}||85;
`mkdir -p $outputDir`;
@@ -1952,7 +1952,7 @@ sub runSpadesAssembly
my $pairFile=shift;
my $unpairFile=shift;
my $time=time();
my $outputDir="$outDir/AssemblyBasedAnalysis";
my $outputDir="$abs_outDir/AssemblyBasedAnalysis";
my $SPAdesOutDir="$outputDir/SPAdes";
my $contig_file= "$outputDir/contigs.fa";
my $contig_for_annotation = "$outputDir/contigs_${contig_size_for_annotation}up.fa";
@@ -2036,7 +2036,7 @@ sub runIdbaAssembly
my $QCoutDir="$outDir/QcReads";;
my $QCstatsFile="$QCoutDir/QC.stats.txt";
my $FastqCountFile="$QCoutDir/fastqCount.txt";
my $outputDir="$outDir/AssemblyBasedAnalysis";
my $outputDir="$abs_outDir/AssemblyBasedAnalysis";
my $pairFastaFile="$outputDir/pairedForAssembly.fasta";
my $unpairFastaFile="$outputDir/unpairedForAssembly.fasta";
my $contig_file= "$outputDir/contigs.fa";
@@ -2516,7 +2516,7 @@ sub download_reads
my @urls = @_;
my $size_limit="3125000000"; # 25G
my $time=time();
my $outputDir = "$outDir/DownloadedReads";
my $outputDir = "$abs_outDir/DownloadedReads";
if ($noColorLog)
{
&lprint ("[Download Fastq]\n");

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