@sjcrh/proteinpaint-server 2.17.0 → 2.18.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/genome/hg38.js +5 -3
- package/package.json +8 -7
- package/server.js +1 -1
- package/utils/fastclust.R +16 -6
package/genome/hg38.js
CHANGED
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@@ -1,6 +1,6 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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-
var
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3
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+
var clinvar_1 = require("../dataset/clinvar");
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exports.default = {
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species: 'human',
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genomefile: 'genomes/hg38.gz',
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@@ -12,7 +12,9 @@ exports.default = {
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label: 'MSigDB',
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cohort: {
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db: { file: 'anno/msigdb/db' },
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15
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-
termdb: {
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15
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+
termdb: {
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16
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isGeneSetTermdb: true
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}
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}
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}
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},
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@@ -30,7 +32,7 @@ exports.default = {
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clinvarVCF: {
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file: 'hg38/clinvar.hg38.hgvs_short.vep.bcf.gz',
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infokey: 'CLNSIG',
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-
categories:
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+
categories: clinvar_1.clinsig
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},
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tracks: [
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{
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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{
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"name": "@sjcrh/proteinpaint-server",
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-
"version": "2.
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"version": "2.18.1",
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"description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
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"main": "server.js",
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"bin": "start.js",
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@@ -10,13 +10,13 @@
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},
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"scripts": {
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"dev": "webpack --env NODE_ENV=development --watch --color",
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-
"start": "tsc genome/*.ts dataset/*.ts && nodemon --enable-source-maps server.js --watch ./server*.js* --watch dataset/*.ts --watch genome/*.ts",
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-
"pretest": "tsc genome/*.ts dataset/*.ts && ./test/pretest.js",
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"start": "tsc --esModuleInterop genome/*.ts dataset/*.ts && nodemon --enable-source-maps server.js --watch ./server*.js* --watch dataset/*.ts --watch genome/*.ts",
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"pretest": "tsc --esModuleInterop genome/*.ts dataset/*.ts && ./test/pretest.js",
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"test": "webpack --env NODE_ENV=test exportsFilename=all-test-context.js && node --enable-source-maps test/serverTests.js",
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16
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-
"test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && tsc dataset/*.ts && node --enable-source-maps test/serverTests.js",
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-
"pretest:integration": "tsc genome/*.ts dataset/*.ts",
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16
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"test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && tsc --esModuleInterop dataset/*.ts && node --enable-source-maps test/serverTests.js",
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"pretest:integration": "tsc --esModuleInterop genome/*.ts dataset/*.ts",
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"test:integration": "echo 'TODO: server integration tests'",
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-
"prepack": "tsc genome/*.ts dataset/*.ts && webpack --env NODE_ENV=production",
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"prepack": "tsc --esModuleInterop genome/*.ts dataset/*.ts && webpack --env NODE_ENV=production",
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"response": "nodemon modules/test/test.server.js --watch src",
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"getconf": "../build/getConfigProp.js"
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},
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@@ -32,9 +32,10 @@
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"babel-loader": "^8.2.2",
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"node-watch": "^0.7.1",
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"nodemon": "^2.0.19",
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-
"prettier": "
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"prettier": "^2.8.8",
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"tape": "^5.2.2",
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"typescript": "^5.0.3",
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"@typescript-eslint/eslint-plugin": "^5.60.0",
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"webpack": "^5.76.0",
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"webpack-cli": "^4.9.2",
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"webpack-node-externals": "^3.0.0",
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