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package.json
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package.json
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{
"name": "aminosee",
"version": "1.33.0",
"owner": "Thomas Bieder Atkinson",
"author": "Tom Atkinson <[email protected]>",
"website": "http://aminosee.funk.nz",
"license": "GPL-3.0-only",
"repository": {
"type": "git",
"url": "git://github.com/tomachinz/AminoSee.git"
},
"description": "A unique visualisation of any large chunk of DNA or RNA residing in ASCII text files (such as FASTA, GBK etc and also just .txt like my hand-made test files), AminoSee is a way to render huge genomics files into a left-to-right top-bottom PNG linear image, a 2D infinite space filling square curve from 18th century, and a 3D hilbert curve from this century! Computation is done locally, without the files leaving your machine. A back-end terminal daemon cli command that can be scripted is combined with a front-end GUI using the Carlo, AminoSee features asynchronous streaming processing enabling arbitrary size files to be processed. It has been tested with files in excess of 4 GB and does not need the whole file in memory at any time. Try running aminosee * in a directory with DNA files, or better run the batch script batch-peptides.sh. The folder dna is provided for bulk rendering it already has those scripts present. The GUI is not finished at this time. it is using THREEjs and a 3D Hilbert Curve, Carlo. Command line options allow one to filter by peptide, for example aminosee * --peptide=Ochre. Allows genomics researchers to convert any file containing blocks of text format DNA (Fasta, GBK, .txt) into an interactive experience.",
"main": "./bin/aminosee",
"bin": {
"aminosee": "./bin/aminosee"
},
"build": {
"productName": "aminosee",
"appId": "nz.funk.aminosee",
"copyright": "Copyright © 2018-2020 Tom Atkinson",
"icon": "src/public/favicon.png",
"directories": [
"src/public/*",
"src/*"
],
"mac": {
"category": [
"public.app-category.education",
"public.app-category.medical"
]
}
},
"scripts": {
"postpublish": "PACKAGE_VERSION=$(cat package.json | grep \\\"version\\\" | head -1 | awk -F: '{ print $2 }' | sed 's/[\",]//g' | tr -d '[[:space:]]') && git tag v$PACKAGE_VERSION && git push --tags",
"cypress": "node_modules/.bin/cypress open",
"demo": "node bin/aminosee demo",
"credits": "./build-credits.sh",
"clean": "rimraf ./dist ./build",
"debug": "node --inspect 27MB_TestPattern.txt --peptide=Ochre 3MB_TestPattern.txt 50KB_TestPattern.txt batch-peptides.sh batch-process.sh Gorilla_gorGor4_chr2B.fa",
"eslint": "eslint -c .eslintrc.js src/aminosee-cli.js > test/eslint-errors.txt ; tail -n 64 test/eslint-errors.txt ; cat test/eslint-errors.txt | wc ",
"gource": "./gource.sh",
"test": "echo 'requires cli programs: time, lighthouse, vows etc' ; time ./run-test.sh --quiet ;",
"start": "node bin/aminosee",
"serve": "node ./bin/aminosee",
"inspect": "node --inspect bin/aminosee dna/27MB_TestPattern.txt /Volumes/aminosee/dna/Brown_Kiwi_NW_013982187v1.fa /Volumes/aminosee/dna/Brown_Kiwi_NW_013982187v1.fa -f -c1000 -vd --debug",
"inspect2": "node --inspect bin/aminosee dna/50KB_TestPattern.txt -f -vd --debug",
"build": "nice npm run build-web ; nice time npm run macos",
"build-all": "./run-test.sh --quiet ; ./build-web.sh ; npm run pkg; ",
"build-web": "npm run credits; npm run genversion ; npm run browserify ; npm run minify ;",
"genversion": "genversion src/aminosee-version.js",
"browserify": "echo DISABLED browserify bin/aminosee -o bin/aminosee.bundle.js",
"minify": "echo DISABLED uglify bin/aminosee.bundle.js -o bin/aminosee.min.js",
"update": "./update.sh",
"pkg": "nice npm run win32 ; nice npm run _macos ; nice npm run _linux ; nice npm run _win64; nice npm run zip",
"zip": "zip -8 -r ./dist/AminoSee_macos.zip ./dist/AminoSee_macos ; nice zip -8 -r ./dist/AminoSee_win.zip ./dist/AminoSee_win ; nice zip -8 -r ./dist/AminoSee_linux.zip ./dist/AminoSee_linux",
"runmac": "time ./dist/AminoSee_macos/aminosee --demo -m9",
"runlinux": "open ./dist/AminoSee_linux/aminosee --test -m9",
"macos": "echo MACOS ; pkg . --build --targets macos --output ./dist/AminoSee_macos/aminosee ; ./dist/AminoSee_macos/aminosee",
"win32": "echo WIN32 ; pkg . --targets win-x86 --output ./dist/AminoSee_win/aminosee-win32.exe",
"win64": "echo WIN64 ; pkg . --targets win-x64 --output ./dist/AminoSee_win/aminosee.exe",
"linux": "echo LINUX ; pkg . --targets linux --output ./dist/AminoSee_linux/aminosee ; ./dist/AminoSee_linux/aminosee",
"_macos": "echo MACOS ; pkg . --targets macos --output ./dist/AminoSee_macos/aminosee ; zip -8 -r ./dist/AminoSee_macos.zip ./dist/AminoSee_macos",
"_win32": "echo WIN32 ; pkg . --targets win-x86 --output ./dist/AminoSee_win/aminosee-win32.exe ;",
"_win64": "echo WIN64 ; pkg . --targets win-x64 --output ./dist/AminoSee_win/aminosee.exe ; zip -8 -r ./dist/AminoSee_win.zip ./dist/AminoSee_win",
"_linux": "echo LINUX ; pkg . --targets linux --output ./dist/AminoSee_linux/aminosee ; zip -8 -r ./dist/AminoSee_linux.zip ./dist/AminoSee_linux"
},
"dependencies": {
"@neutralinojs/neu": "^1.7.0",
"async-kit": "^2.2.4",
"autocannon": "^4.6.0",
"bcrypt": "^5.0.0",
"chalk": "^2.4.2",
"describe": "^1.2.0",
"execa": "^5.1.1",
"fs-extra": "^8.1.0",
"genversion": "^2.2.1",
"hammerjs": "^2.0.8",
"hilbert-2d": "0.0.1",
"http-server": "^0.12.3",
"internal-ip": "^4.3.0",
"json-beautify": "^1.1.1",
"lighthouse": "^8.1.0",
"node-fetch": "^2.6.1",
"open": "^6.4.0",
"parallax-js": "^3.1.0",
"phoenix": "^1.5.6",
"preferences": "^1.0.2",
"terminal-kit": "^1.43.0",
"three": "^0.118.3",
"vows": "^0.8.3",
"xmlhttprequest": "^1.8.0",
"xterm": "^4.9.0"
},
"devDependencies": {
"@gmod/indexedfasta": "^1.0.13",
"ascii-histogram": "^1.2.1",
"async": "^3.2.0",
"async-kit": "^2.2.4",
"body-parser": "^1.19.0",
"browser-resolve": "^1.11.3",
"browserify": "^16.5.2",
"bytes": "^3.1.0",
"carlo": "^0.9.46",
"cross-spawn": "^6.0.5",
"cucumber": "^5.1.0",
"cypress": "^5.4.0",
"dat.gui": "^0.7.7",
"ecstatic": "^4.1.4",
"eslint": "^7.11.0",
"eslint-config-rallycoding": "^3.2.0",
"event-stream": "^4.0.1",
"hilbert-2d": "0.0.1",
"humanize-duration": "^3.24.0",
"husky": "^3.1.0",
"internal-ip": "^4.3.0",
"json-beautify": "^1.1.1",
"keypress": "^0.2.1",
"lazyness": "^1.2.0",
"local-web-server": "^4.2.1",
"minimist": "^1.2.5",
"node-gyp": "^5.1.1",
"node-pty": "^0.8.1",
"npm-merge-driver": "^2.3.6",
"parse-apache-directory-index": "^1.2.1",
"pkg": "^4.4.9",
"png.js": "^0.2.1",
"pngjs": "^3.4.0",
"remove": "^0.1.5",
"request": "^2.88.2",
"save": "^2.4.0",
"serve": "^11.3.2",
"serve-handler": "^6.1.3",
"sliced": "^1.0.1",
"spdy": "^4.0.2",
"stream-file": "^0.2.4",
"systeminformation": "^4.27.9",
"tcp-port-used": "^1.0.1",
"through": "^2.3.8",
"uniq": "^1.0.1",
"webpack-node-externals": "^1.7.2",
"xmlhttprequest": "^1.8.0"
},
"keywords": [
"dna",
"genomics",
"visualisation",
"renderer",
"genetics",
"bioinformatics",
"bionode",
"amino acids",
"peptides",
"codons"
],
"pkg": {
"targets": [
"node10",
"linux",
"macos",
"win"
],
"scripts": [],
"assets": [
"node_modules/terminal-kit/lib/Palette.js",
"node_modules/terminal-kit/lib/image.js",
"node_modules/hilbert-2d/hilbert.js",
"node_modules/terminal-kit/lib/termconfig",
"node_modules/terminal-kit/lib/colorScheme",
"node_modules/open/xdg-open",
"src/*",
"src/public/*",
"package.json"
]
}
}