[
    {
        "id": "igv_visualize",
        "name": "IGV visualize",
        "article": "10.1038\/nbt.1754",
        "website": "https:\/\/software.broadinstitute.org\/software\/igv\/",
        "git": "https:\/\/github.com\/igvteam\/igv",
        "description": "Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations ",
        "version": "2.13.2",
        "documentation": "https:\/\/software.broadinstitute.org\/software\/igv\/",
        "multiqc": "custom",
        "commands": [
            {
                "name": "igv_visualize",
                "cname": "Igv visualize",
                "command": "igv",
                "category": "visualization",
                "output_dir": "igv_visualize",
                "inputs": [
                    {
                        "name": "genome",
                        "type": "contigs",
                        "file": ""
                    },
                    {
                        "name": "circos_bam",
                        "type": "bams"
                    }
                ],
                "outputs": [
                    {
                        "name": "igv_png",
                        "type": "png",
                        "file": "{sample}_{contig_name}_mqc.png",
                        "description": "Contig and read coverage visualisation"
                    }
                ],
                "options": [
                    {
                        "name": "igv_visualize_threads",
                        "prefix": "--thread_number",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "IGV": [
                "Robinson, J., Thorvaldsd\u00f3ttir, H., Winckler, W. et al. Integrative genomics viewer. Nat Biotechnol 29, 24-26 (2011). https:\/\/doi.org\/10.1038\/nbt.1754"
            ],
            "samtools": [
                "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352"
            ]
        },
        "yaml": "{\n  id: igv_visualize,\n  name: IGV visualize,\n  article: '10.1038\/nbt.1754',\n  website: 'https:\/\/software.broadinstitute.org\/software\/igv\/',\n  git: 'https:\/\/github.com\/igvteam\/igv',\n  description: 'Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations ',\n  version: '2.13.2',\n  documentation: 'https:\/\/software.broadinstitute.org\/software\/igv\/',\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: igv_visualize,\n        cname: \"Igv visualize\",\n        command: 'igv',\n        category: \"visualization\",\n        output_dir: igv_visualize,\n        inputs: [{ name: genome, type: \"contigs\",file: \"\"},{ name: circos_bam, type: \"bams\" }],\n        outputs:\n          [\n            { name: igv_png, type: \"png\", file: \"{sample}_{contig_name}_mqc.png\", description: \"Contig and read coverage visualisation\" },\n          ],\n        options:\n          [\n            {\n              name: igv_visualize_threads,\n              prefix: --thread_number,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # xvfb: [\n    #   \"apt-get install -y xvfb\",\n    # ],\n    # samtools: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n    #   \"tar -xvjf samtools-1.9.tar.bz2\",\n    #   \"cd samtools-1.9\",\n    #   \".\/configure && make\",\n    #   \"cd ..\",\n    #   \"mv samtools-1.9\/samtools bin\/samtools\",\n    #   \"rm -r samtools-1.9 samtools-1.9.tar.bz2\"\n    # ],\n    # IGV:\n    # [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget -c https:\/\/data.broadinstitute.org\/igv\/projects\/downloads\/2.6\/IGV_Linux_2.6.2.zip\",\n    #   \"unzip IGV_Linux_2.6.2.zip\",\n    #   \"rm IGV_Linux_2.6.2.zip\",\n    #   \"ENV PATH \/opt\/biotools\/IGV_Linux_2.6.2:$PATH\",\n    #   \"sed -i 's\/-Xmx4g\/-Xmx16g\/' \/opt\/biotools\/IGV_Linux_2.6.2\/igv.sh\"\n    # ],\n  },\n  citations:  {\n    IGV: [\n      \"Robinson, J., Thorvaldsd\u00f3ttir, H., Winckler, W. et al. Integrative genomics viewer. Nat Biotechnol 29, 24-26 (2011). https:\/\/doi.org\/10.1038\/nbt.1754\"\n    ],\n    samtools: [\n      \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n    ]\n  }\n}"
    }
]