@sjcrh/proteinpaint-server 2.30.4 → 2.30.5

package/cards/index.json

@@ -1,327 +0,0 @@
-{
-    "columnsLayout": [
-        {
-            "gridarea": "col1",
-            "sections": [
-                {
-                    "id": "tracks",
-                    "name": "Tracks"
-                }
-            ]
-        },
-        {
-            "gridarea": "col2",
-            "sections": [
-                {
-                    "id": "datasetButtons",
-                    "name": "Featured Datasets"
-                },
-                {
-                    "id": "apps",
-                    "name": "Launch Apps"
-                },
-                {
-                    "id": "nestedCards"
-                }
-            ]
-        }
-    ],
-    "elements": [
-        {
-            "type": "nestedCard",
-            "name": "Use Cases",
-            "section": "nestedCards",
-            "description": "find workflows and processes for specific needs",
-            "children": [
-                {
-                    "name": "Generate GenomePaint SV View",
-                    "type": "card",
-                    "description": "Create a SV view with BigWig tracks using Python script",
-                    "sandboxHtml": "svview"
-                },
-                {
-                    "name": "DNAnexus Tips",
-                    "type": "card",
-                    "description": "Guide to use DNAnexus for ProteinPaint",
-                    "sandboxHtml": "dnanexusTips"
-                }
-            ]
-        },
-        {
-            "type": "card",
-            "name": "GenomePaint",
-            "section": "tracks",
-            "description": "Explore coding and non-coding variants in cancer",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/gpaint-square.png",
-            "sandboxJson": "genomepaint",
-            "searchterms": ["GenomePaint"]
-        },
-        {
-            "type": "card",
-            "name": "BigWig",
-            "section": "tracks",
-            "description": "Quantitative data at genomic positions",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/bigwig-square.png",
-            "sandboxJson": "bigwig",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "JSON BED",
-            "section": "tracks",
-            "description": "Genomic feature annotation",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/bedj-square.png",
-            "sandboxJson": "bedj",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "Allelic imbalance",
-            "section": "tracks",
-            "description": "From tumor and germline DNA",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/aicheck-square.png",
-            "sandboxJson": "ai",
-            "searchterms": ["aicheck", "tumor", "normal", "DNA"]
-        },
-        {
-            "type": "card",
-            "name": "Profile gene value",
-            "section": "tracks",
-            "description": "Profiling results & gene-level values",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/pgv-square.png",
-            "sandboxJson": "pgv",
-            "searchterms": ["pgv", "chromHMM", "profiling results", "gene level", "gene expression"]
-        },
-        {
-            "type": "card",
-            "name": "Expression rank",
-            "section": "tracks",
-            "description": "Against all samples from a cohort",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/exprank-square.png",
-            "sandboxJson": "exprank",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "Hi-C",
-            "section": "tracks",
-            "description": "Chromatin interaction at a locus",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/hic-square.png",
-            "ribbon": { "text": "updated", "expireDate": "2023-10-31" },
-            "sandboxJson": "hic",
-            "searchterms": ["hic", "hicstraw", "chromatin interaction", "conformation"]
-        },
-        {
-            "type": "card",
-            "name": "Lollipop",
-            "section": "tracks",
-            "description": "Coding mutations and gene fusions",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/lollipop-square.png",
-            "sandboxJson": "lollipop",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "Splice Junction",
-            "section": "tracks",
-            "description": "Single sample and cohort",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/junction-cohort-square.png",
-            "sandboxJson": "junction",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "Track list & facet table",
-            "section": "tracks",
-            "description": " ",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/tklist-square.png",
-            "sandboxJson": "tklist",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "Arc Track",
-            "section": "tracks",
-            "description": "Pairwise chromatin interactions",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/arc-square.png",
-            "sandboxJson":"arc",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "ASE",
-            "section": "tracks",
-            "ribbon": {"text": "beta"},
-            "description": "Allele-specific expression analysis",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/ase-square.png",
-            "sandboxJson": "ase",
-            "searchterms": ["Allele-specific gene expression"]
-        },
-        {
-            "type": "card",
-            "name": "Gene Fusion",
-            "section": "tracks",
-            "description": " ",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/genefusion-square.png",
-            "sandboxJson": "genefusion",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "BAM",
-            "section": "tracks",
-            "description": "Sequence reads alignment",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/bam-square.png",
-            "sandboxJson": "bam",
-            "searchterms": ["BLAT"]
-        },
-        {
-            "type": "card",
-            "name": "Bampile",
-            "hidden": true,
-            "section": "tracks",
-            "ribbon": {"text": "beta"},
-            "description": "Deep sequencing",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/bampile-square.png",
-            "sandboxJson": "bampile",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "GDC BAM slicing",
-            "section": "tracks",
-            "disableTopTabs": true,
-            "description": "Visualize sequencing reads in NCI GDC",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/bam-square.png",
-            "sandboxJson": "gdcbam",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "Additional Track Features",
-            "section": "tracks",
-            "description": "ProteinPaint arguments applicable to any track",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/code-square.png",
-            "sandboxJson": "tkFeatures",
-            "searchterms": []
-        },
-        {
-            "type": "card",
-            "name": "FusionEditor",
-            "section": "apps",
-            "description": "Review CICERO output",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/fusion-editor-square.png",
-            "sandboxJson": "fusioneditor",
-            "searchterms": ["CICERO"]
-        },
-        {
-            "type": "card",
-            "name": "2DMAF",
-            "section": "apps",
-            "description": "Somatic mutations from diagnosis & relapse",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/2dmaf-square.png",
-            "sandboxJson": "2dmaf",
-            "searchterms": ["2dmaf", "clonal evolution", "point mutations"]
-        },
-        {
-            "type": "card",
-            "name": "Load mutations from text files",
-            "section": "apps",
-            "description": "Mutation heatmap",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/heatmap-square.png",
-            "sandboxJson": "study",
-            "searchterms": ["heat map", "oncoprint"]
-        },
-        {
-            "type": "card",
-            "name": "MA+Volcano plots",
-            "section": "apps",
-            "description": "Differential gene expression",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/mavb-square.png",
-            "sandboxJson": "mavb",
-            "searchterms": ["differential gene expression", "RNAseq coverage"]
-        },
-        {
-            "type": "card",
-            "name": "MAF-timeline",
-            "section": "apps",
-            "hidden": true, 
-            "description": "Mutant allele fraction timeline chart by date",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/maf-timeline-square.png",
-            "sandboxJson": "maf.timeline",
-            "searchterms": ["mutant allele fraction", "snv", "snv4"]
-        },
-        {
-            "type": "dsButton",
-            "name": "Pediatric Cancer Mutation",
-            "section": "datasetButtons",
-            "sandboxJson": "pcmBtn",
-            "searchterms": ["pcgp", "Pan-TARGET", "T-ALL cohort"]
-        },
-        {
-            "type": "dsButton",
-            "name": "Pediatric2 GenomePaint",
-            "section": "datasetButtons",
-            "sandboxJson": "ped2Btn",
-            "searchterms": ["relapsed ALL cohort", "Genome for Kids", "g4k", "Pan-neuroblastoma analysis"]
-        },
-        {
-            "type": "dsButton",
-            "name": "NCI GDC",
-            "section": "datasetButtons",
-            "sandboxJson": "nciGdcBtn",
-            "searchterms": ["TCGA", "CPTAC", "TARGET"]
-        },
-        {
-            "type": "dsButton",
-            "name": "CIViC",
-            "section": "datasetButtons",
-            "sandboxJson": "civicBtn"
-        },
-        {
-            "type": "dsButton",
-            "name": "Survivorship Study",
-            "section": "datasetButtons",
-            "sandboxJson": "survivorBtn",
-            "searchterms": ["sjlife", "ccss", "St Jude Life", "Childhood Cancer Survivor Study"]
-        },
-        {
-            "type": "card",
-            "name": "Scatter Plot",
-            "section": "apps",
-            "description": "2D scatter plot of samples & metadata",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/scatterplot-square.png",
-            "sandboxJson": "scatterplot",
-            "searchterms": ["tSNE", "lasso"]
-        },
-        {
-            "type": "card",
-            "name": "Single Cell",
-            "section": "apps",
-            "description": "Single-cell omics viewer",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/singlecell-square.png",
-            "sandboxJson": "singlecell",
-            "searchterms": ["tsne", "gene expression", "multi-gene heatmap", "violin plot", "box plot", "umap"]
-        },
-        {
-            "type": "card",
-            "name": "Data Browser",
-            "section": "apps",
-            "description": "Browse data from a custom cohort",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/databrowser-square.png",
-            "ribbon": {"text":"beta"},
-            "sandboxJson": "databrowser",
-            "searchterms": ["clinical", "dictionary"]
-        },
-        {
-            "type": "card",
-            "name": "Disco Plot",
-            "section": "apps",
-            "description": "Circos-like plot of genome-wide mutational events",
-            "image": "https://proteinpaint.stjude.org/ppdemo/images/disco-square.png",
-            "ribbon": { "text":"new", "expireDate": "2023-10-31" },
-            "sandboxJson": "disco",
-            "searchterms": ["disco"]
-        }
-    ]
-}

package/cards/junction.json

@@ -1,98 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "label": "A sample splice junction",
-            "download":"https://proteinpaint.stjude.org/ppdemo/hg19/junction/junctionDemoData.tar.gz",
-            "urlparam": "?block=on&genome=hg19&junctionfile=RNA%20splice%20junction,proteinpaint_demo/hg19/junction/file.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/junction/file.gz",
-                    "tabixQueryCoord": "chr17:7568451-7591984"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "nativetracks":"refgene",
-                "tracks": [{
-                    "type": "junction",
-                    "file": "proteinpaint_demo/hg19/junction/file.gz",
-                    "name": "RNA splice junction demo"
-                }]
-            },
-            "testSpec": {
-                "expected": {"circle": 15, "line": 15}
-            }
-        },
-        {
-            "label":"Cohort from an External JSON",
-            "message": "",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/junction/junctionJsonDemoData.tar.gz",
-            "urlparam": "?genome=hg19&block=1&mdsjunctionfile=Demo,proteinpaint_demo/hg19/junction/json.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/junction/json.gz",
-                    "tabixQueryCoord": "chr17:7568451-7591984"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "nobox": 1,
-                "noheader": 1,
-                "block":1,
-                "genome": "hg19",
-                "nativetracks": "Refgene",
-                "tracks": [{
-                    "type": "mdsjunction",
-                    "name": "Cohort splice junction Demo",
-                    "file": "proteinpaint_demo/hg19/junction/json.gz"
-                }]
-            },
-            "testSpec": {
-                "expected": {"circle": 15, "line": 15}
-            }
-        },
-        {
-            "label":"Cohort from a JSON Matrix File",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/junction/junctionMatrixDemoData.tar.gz",
-            "urlparam": "?genome=hg19&block=1&junctionmatrix=test,proteinpaint_demo/hg19/junction/matrix.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/junction/matrix.gz",
-                    "tabixQueryCoord": "chr17:7568451-7591984"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "nobox": 1,
-                "noheader": 1,
-                "block":1,
-                "genome": "hg19",
-                "nativetracks": "Refgene",
-                "tracks": [{
-                    "type": "mdsjunction",
-                    "name": "Cohort matrix splice junction demo",
-                    "file2": "proteinpaint_demo/hg19/junction/matrix.gz"
-                }]
-            },
-            "buttons": [
-                {
-                    "name": "Download Matrix Script",
-                    "download": "https://proteinpaint.stjude.org/ppdemo/scripts/rnapeg2matrix.py.gz"
-                }
-            ],
-            "testSpec": {
-                 "expected": {"circle": 15, "line": 15}
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1PFva3Mn-U4VPNW0vHHC-CSnYBeotRnqbhCMQPmyLQG4/edit"
-        }
-    ]
-}