[
    {
        "id": "beast",
        "name": "BEAST",
        "article": "DOI:10.1371\/journal.pcbi.1006650",
        "website": "https:\/\/www.beast2.org\/",
        "git": "http:\/\/www.github.com\/CompEvol\/beast2",
        "description": "BEAST 2: cross-platform program for Bayesian phylogenetic analysis of molecular sequences",
        "version": "2.6.3",
        "documentation": "https:\/\/www.beast2.org\/tutorials\/",
        "multiqc": "custom",
        "commands": [
            {
                "name": "beast",
                "cname": "beast",
                "command": "beast",
                "category": "phylogenetics",
                "output_dir": "beast",
                "inputs": [
                    {
                        "name": "beast_xml",
                        "type": "xml",
                        "description": "Beast compatible file with sequences and data"
                    }
                ],
                "outputs": [
                    {
                        "name": "beast_trees",
                        "type": "nexus",
                        "file": "beast.trees",
                        "description": "sampled trees"
                    },
                    {
                        "name": "log",
                        "type": "txt",
                        "file": "beast.log",
                        "description": "beast log"
                    }
                ],
                "options": [
                    {
                        "name": "beast_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "beast_seed",
                        "prefix": "--seed",
                        "type": "numeric",
                        "value": 1234,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "seed for pseudo-random number generator"
                    }
                ]
            }
        ],
        "install": [],
        "assets": [
            "figtree.jar"
        ],
        "citations": {
            "beast": [
                "Bouckaert R., Vaughan T.G., Barido-Sottani J., Duch\u00eane S., Fourment M., Gavryushkina A., et al. (2019) BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology, 15(4), e1006650"
            ]
        },
        "yaml": "{\n  id: beast,\n  name: BEAST,\n  article: \"DOI:10.1371\/journal.pcbi.1006650\",\n  website: \"https:\/\/www.beast2.org\/\",\n  git: \"http:\/\/www.github.com\/CompEvol\/beast2\",\n  description: \"BEAST 2: cross-platform program for Bayesian phylogenetic analysis of molecular sequences\",\n  version: \"2.6.3\",\n  documentation: \"https:\/\/www.beast2.org\/tutorials\/\",\n  multiqc:  \"custom\",\n  commands:\n    [\n      {\n        name: \"beast\",\n        cname: \"beast\",\n        command: \"beast\",\n        category: \"phylogenetics\",\n        output_dir: \"beast\",\n        inputs: [\n          { name: beast_xml, type: \"xml\", description: \"Beast compatible file with sequences and data\" },\n        ],\n        outputs:\n        [\n          { name: \"beast_trees\", type: \"nexus\", file: \"beast.trees\", description: \"sampled trees\" },\n          { name: \"log\", type: \"txt\", file: \"beast.log\", description: \"beast log\" },\n        ],\n        options:\n          [\n            {\n              name: beast_threads,\n              prefix: \"--threads\",\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              name: beast_seed,\n              prefix: \"--seed\",\n              type: numeric,\n              value: 1234,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"seed for pseudo-random number generator\",\n            },\n    \n          ],\n      },\n    ],\n  install: {\n    # beast: [\n    #   \"cd \/opt\/biotools\/\",\n    #   \"wget https:\/\/github.com\/CompEvol\/beast2\/releases\/download\/v2.6.7\/BEAST.v2.6.7.Linux.tgz\",\n    #   \"tar -zxvf BEAST.v2.6.7.Linux.tgz\",\n    #   \"rm -f BEAST.v2.6.7.Linux.tgz\",\n    #   \"beast\/bin\/packagemanager -add SSM\",\n    #   \"echo 'export PATH=\/opt\/biotools\/beast\/bin:$PATH' >> \/etc\/environment\"\n    # ],\n    # java8: [\n    #   \"apt-get install -y openjdk-8-jre\",\n    #   \"apt-get install -y openjdk-8-jdk\" \n    # ],\n    # beagle: [\n    # \"cd \/opt\/biotools\",\n    # \"git clone --depth=1 https:\/\/github.com\/beagle-dev\/beagle-lib.git\",\n    # \"cd beagle-lib\",\n    # \"mkdir build && cd build\",\n    # \"cmake  ..\",\n    # \"make install\",\n    # \"echo 'export LD_LIBRARY_PATH=\/usr\/local\/lib:$LD_LIBRARY_PATH' >> \/etc\/environment\"\n    # ],\n    # imagemagick: [\n    #  \"apt-get install imagemagick \"\n    # ]\n  },\n  assets:  [\"figtree.jar\"],\n  citations:  {\n    beast: [\n    \"Bouckaert R., Vaughan T.G., Barido-Sottani J., Duch\u00eane S., Fourment M., Gavryushkina A., et al. (2019) BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology, 15(4), e1006650\"\n    ]\n  }\n}\n"
    }
]