diff --git a/eb/DigitalBarcodeReadgroups-0.1.2-goolf-1.7.20-Perl-5.20.2-bare.eb b/eb/DigitalBarcodeReadgroups-0.1.2-goolf-1.7.20-Perl-5.20.2-bare.eb new file mode 100644 index 0000000..20d4a23 --- /dev/null +++ b/eb/DigitalBarcodeReadgroups-0.1.2-goolf-1.7.20-Perl-5.20.2-bare.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'DigitalBarcodeReadgroups' +version = '0.1.2' + +homepage = 'https://github.com/mmterpstra/%s' % (name) +description = """Misc tools""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [('https://github.com/mmterpstra/%s/archive/' % (name) )] +sources = [ '%s.tar.gz' % version ] + +perl = 'Perl' +perlver = '5.20.2' +perlversuffix = '-bare' +versionsuffix = '-%s-%s%s' % (perl, perlver, perlversuffix) + +samtools='SAMtools' +samtoolsver='1.2' + +dependencies = [ + (perl, perlver, perlversuffix), + (samtools, samtoolsver), +] + +# +# Check if all binaries are present. +# + +sanity_check_paths = { + 'files': [ 'src/NugeneDigitalSplitter.pl', 'src/NugeneMergeFastqFiles.pl' ], + 'dirs': [ 'src/' ], +} + +moduleclass = 'bio' diff --git a/src/NugeneMergeFastqFiles.pl b/src/NugeneMergeFastqFiles.pl index 5284ac7..0bd999d 100644 --- a/src/NugeneMergeFastqFiles.pl +++ b/src/NugeneMergeFastqFiles.pl @@ -44,7 +44,7 @@ sub main { #if reading record fails from both fq files then end - while( ((((defined($ARGV[3]) && ! -e $ARGV[3] )|| (my $fq2 = ReadFastq(\$fastq2Handle) ))) && (my $fq1 = ReadFastq(\$fastq1Handle))) && (my $rfq = ReadFastq(\$randomBcHandle)) ){ + while( ((((not(defined($ARGV[3])))|| (my $fq2 = ReadFastq(\$fastq2Handle) ))) && (my $fq1 = ReadFastq(\$fastq1Handle))) && (my $rfq = ReadFastq(\$randomBcHandle)) ){ warn $.if $. =~ /00000$/; my $rbc = $rfq->[1];