Dependencies

1) Dependency tree

- BWA (0.7.15)
- sambamba (v0.6.6)
- GATK (3.7)
- io_lib (1.14.6)
- Python (2.7.10)
- Zlib (1.2.8)
- bzip2 (1.0.6)
- libreadline (6.3)
    o ncursus (5.9)
- Picard (2.9.0)
    o R(3.3.1)
        • libreadline (6.3)
        • ncursus (5.9)
        • libjpeg-turbo (1.4.2)
        • NASM(2.11.08)
        • LibTIFF (4.0.4)
        • Tk (8.6.4)
            o Tcl (8.6.4.) 
                • Zlib (1.2.8)
        • cUrl (7.47.1)
        • libxml2 (2.9.2)
        • cairo (1.14.6)
            o bzip2 (1.0.6)
            o pixman (0.32.8)
            o fontconfig (2.11.94)
                • freetype (2.6.1)
                    o libpng (1.6.21)
                        • zlib (1.2.8)
                    o expat (2.1.0)
        • PCRE (8.38)
        • Java (1.8.0_45)
    o Java (1.7.0_80)
- HTSlib(1.3.2)
- cutadapt (1.9.1)
- ngs-utils (16.12.1)
    o Text-CSV (1.33)
    o Log-Log4Perl (1.46)
- Molgenis-Compute (16.08.1)
- CmdLineAnnotator (1.9.0)

2) NGS_DNA-3.4.0 pipeline dependencies

('BWA', '0.7.15', '', ('foss', '2015b')),
('BEDTools', '2.25.0', '', ('foss', '2015b')),
('CoNVaDING', '1.1.6', '', ('dummy', '')),
('Molgenis-Compute', 'v17.08.1', '-Java-1.8.0_74'),
('FastQC', '0.11.5', '-Java-1.8.0_74'),
('GATK', '3.7', '-Java-1.8.0_74'),
('Gavin-ToolPack', '1.0', '-Java-1.8.0_74'),
('io_lib', '1.14.6', '', ('foss', '2015b')),
('manta','1.2.1', '', ('foss', '2015b')),
('snpEff', '4.3', '-Java-1.7.0_80'),
('ngs-utils', '17.11.1', '', ('dummy', '')),
('PerlPlus', '5.22.0', '-v17.08.1', ('foss', '2015b')),
('pigz', '2.3.1', '', ('foss', '2015b')),
('picard', '2.9.0', '-Java-1.8.0_74'),
('sambamba', 'v0.6.6', '', ('foss', '2015b')),
('seqtk', '1.2', '', ('foss', '2015b')),
('SAMtools', '1.2', '', ('foss', '2015b')),
('HTSlib', '1.3.2', '', ('foss', '2015b')),
('CmdLineAnnotator', '1.21.1', '-Java-1.8.0_45'),
('xhmm', '2016-01-04-cc14e528d909', '', ('foss', '2015b')),
('CADD', 'v1.3', '', ('dummy', '')),
('multiqc', '1.0','-Python-2.7.11', ('foss','2015b')),
('VEP', '90.5', '', ('dummy', '')),