app.json

{
    "id": "wallen-autodock-vina",
    "version": "1.2.3",
    "description": "This application provides an interface for conducting virtual screening for identifying small molecules that bind to your target protein using Autodock Vina docking software. This application is intended to provide easy access to researchers wishing to perform small numbers of docking or virtual screening experiments. Visit the linked documentation page for a tutorial on running a job here.",
    "owner": "${apiUserId}",
    "enabled": true,
    "runtime": "SINGULARITY",
    "runtimeVersion": null,
    "runtimeOptions": [
        "SINGULARITY_RUN"
    ],
    "containerImage": "docker://wjallen/autodock-vina:1.2.3",
    "jobType": "BATCH",
    "maxJobs": -1,
    "maxJobsPerUser": -1,
    "strictFileInputs": false,
    "jobAttributes": {
        "description": "Run Autodock-Vina for virtual screening",
        "dynamicExecSystem": false,
        "execSystemConstraints": null,
        "execSystemId": "ls6",
        "execSystemExecDir": "${JobWorkingDir}",
        "execSystemInputDir": "${JobWorkingDir}",
        "execSystemOutputDir": "${JobWorkingDir}",
        "execSystemLogicalQueue": "normal",
        "archiveSystemId": "ls6",
        "archiveSystemDir": "HOST_EVAL($STOCKYARD)/tapis/archive/${JobCreateDate}/${JobName}-${JobUUID}",
        "archiveOnAppError": true,
        "isMpi": true,
        "mpiCmd": "ibrun",
        "cmdPrefix": null,
        "nodeCount": 1,
        "coresPerNode": 32,
        "memoryMB": 256000,
        "maxMinutes": 2880,
        "subscriptions": [],
        "tags": [],
        "fileInputs": [
            {
                "name": "Protein Receptor Input File",
                "description": "Target protein receptor in .pdb or .pdbqt format",
                "inputMode": "REQUIRED",
                "autoMountLocal": true,
                "sourceUrl": null,
                "targetPath": "*"
            }
        ],
        "fileInputArrays": [],
        "parameterSet": {
            "appArgs": [
                {
                    "name": "Ligand Library",
                    "description": "Select the ligand database to screen.",
                    "inputMode": "REQUIRED",
                    "arg": "/scratch/projects/docking/Test-set-compressed",
                    "notes": {
                        "enum_values": [
                            {"/scratch/projects/docking/Test-set-compressed": "Test-set"},
                            {"/scratch/projects/docking/Enamine-PC-compressed": "Enamine-PC"},
                            {"/scratch/projects/docking/Enamine-AC-compressed": "Enamine-AC"},
                            {"/scratch/projects/docking/Enamine-HTSC-compressed": "Enamine-HTSC"},
                            {"/scratch/projects/docking/ZINC-fragments-compressed": "ZINC-fragments"},
                            {"/scratch/projects/docking/ZINC-in-trials-compressed": "ZINC-in-trials"}
                        ]
                    }
                },
                {
                    "name": "Box Center",
                    "description": "X, Y, Z Cartesian coordinate of the box center (in Angstroms, comma separated, no spaces).",
                    "inputMode": "REQUIRED",
                    "arg": "0,0,0",
                    "notes": {}
                },
                {
                    "name": "Box Size",
                    "description": "Box size in the X,Y,Z dimension (in Angstroms, comma separated, no spaces).",
                    "inputMode": "REQUIRED",
                    "arg": "20,20,20",
                    "notes": {}
                },
                {
                    "name": "Top N Scores",
                    "description": "The number of top scoring docked ligands to be returned (max: 1000)",
                    "inputMode": "REQUIRED",
                    "arg": "500",
                    "notes": {}
                },
                {
                    "name": "Forcefield Selection",
                    "description": "Select whether molecular docking is run using the AutoDock Vina forcefield (vina) or the AutoDock4 forcefield (ad4).",
                    "inputMode": "REQUIRED",
                    "arg": "vina",
                    "notes": {
                        "enum_values": [
                            {"vina": "AutoDock Vina (vina)"},
                            {"ad4": "AutoDock4 (ad4)"}
                        ],
                        "isHidden": true
                    }
                },
                {
                    "name": "Docking Method",
                    "description": "Select whether to use rigid or flexible docking methods. If flexible is chosen, please provide the flexible sidechain names below.",
                    "inputMode": "REQUIRED",
                    "arg": "rigid",
                    "notes": {
                        "enum_values": [
                            {"rigid": "Rigid docking"},
                            {"ad4": "Flexibile docking"}
                        ],
                        "isHidden": true
                    }
                },
                {
                    "name": "Flexible Sidechains",
                    "description": "If using flexible docking, provide the sidechain names with an underscore separating each (e.g. --sidechains ASP363_SER385_TYR393).",
                    "inputMode": "INCLUDE_ON_DEMAND",
                    "arg": null,
                    "notes": {
                        "isHidden": true
                    }
                }
            ],
            "containerArgs": [],
            "schedulerOptions": [
                {
                    "name": "TACC Scheduler Profile",
                    "description": "Scheduler profile for HPC clusters at TACC",
                    "inputMode": "FIXED",
                    "arg": "--tapis-profile tacc-apptainer",
                    "notes": {
                        "isHidden": true
                    }
                }
            ],
            "envVariables": [],
            "archiveFilter": {
                "includes": [],
                "excludes": [],
                "includeLaunchFiles": true
            }
        }

    },
    "tags": [
        "portalName: CEP",
        "portalName: UTRC"
    ],
    "notes": {
        "label": "AutoDock Vina v1.2.3",
        "helpUrl": "https://drugdiscovery.tacc.utexas.edu/",
        "hideNodeCountAndCoresPerNode": false,
        "isInteractive": false,
        "icon": null,
        "category": "Simulation"
    }
}