Workflow

1) Dependency tree

- HTSeq (0.6.1p1-foss-2015b)
- hisat (0.1.5-beta-foss-2015b)
- BBMap (35.69-Java-1.7.0_80)
- FastQC (0.11.3-Java-1.7.0_80)
- io_lib (1.14.6)
- Python (2.7.9)
- Zlib (1.2.8)
- bzip2 (1.0.6)
- libreadline (6.3)
    o ncursus (5.9)
- Picard
    o R(3.2.1-UMCG)
        • 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)
- tabix(0.2.6)
- cutadapt (1.8.1)
- wkhtmltox (0.12.3)
- ngs-utils (16.05.1)
    o Text-CSV (1.33)
    o Log-Log4Perl (1.46)
- Molgenis-Compute (16.05.1)
- CmdLineAnnotator (1.9.0)

2) NGS_RNA-3.2.4 pipeline dependencies

('HTSeq','0.6.1p1-foss-2015b'),
('hisat','0.1.5-beta-foss-2015b'),
('Ghostscript','9.16-foss-2015b'),
('BBMap','35.69-Java-1.7.0_80')    
('CmdLineAnnotator','1.9.0-Java-1.8.0_45')
('cutadapt-1.8.1-foss-2015b-Python-2.7.9'),
('FastQC','0.11.3-Java-1.7.0_80'),
('GATK','3.5-Java-1.7.0_80'),
('io_lib','1.14.6-foss-2015b'),
('Java','1.8.0_45'),
('Molgenis-Compute','v16.05.1-Java-1.8.0_45'),
('ngs-utils','16.05.1'),
('picard','1.130-Java-1.7.0_80'),
('Python','2.7.9-foss-2015b'),
('R','3.2.1-foss-2015b'),
('SAMtools','1.2-foss-2015b'),
('tabix','0.2.6-foss-2015b'),
('wkhtmltox','0.12.3')