Set up docker for genenetwork #29
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| node_modules | ||
| npm-debug.log |
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| FROM node:11.9.0 | ||
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| # Set the working directory to /app | ||
| WORKDIR /app | ||
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| # Copy the current directory contents into the container at /app | ||
| COPY package*.json entrypoint.sh ./ | ||
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| # Install any needed packages specified in requirements.txt | ||
| RUN npm install | ||
| # If you are building your code for production | ||
| # RUN npm ci --only=production | ||
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| # | ||
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| RUN npm build | ||
| RUN npm i natives | ||
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| # Bundle app source | ||
| COPY . . | ||
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| # Make port 80 available to the world outside this container | ||
| EXPOSE 80 | ||
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| # Fill elasticsearch with entrypoint.sh script | ||
| RUN chmod +x entrypoint.sh # if not already executable | ||
| ENTRYPOINT ["/app/entrypoint.sh"] | ||
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| # Run app.py when the container launches | ||
| CMD ["npm", "start"] | ||
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| module.exports = { | ||
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| domain: '' | ||
| }; | ||
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| /** | ||
| * Local environment settings | ||
| * In a production environment, you probably want to leave this file out | ||
| * entirely and leave all your settings in env/production.js | ||
| */ | ||
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| module.exports = { | ||
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| genesToTranscripts: '/app/data/metabrainnetwork/files/genesToTranscripts.txt', | ||
| transcriptMappingFile: 'xxx', | ||
| mim2gene: '/app/data/metabrainnetwork/files/new/mim2gene.txt', | ||
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| geneDescFile: '/app/data/metabrainnetwork/files/new/ENSGToGeneNameHGNCBiotypeChromosomeStartStopStrandAndDescriptionV83FilteredNonChromosomesRemovedDuplicateTranscriptsRemoved.txt', | ||
| genePredScoreFile: '/app/data/metabrainnetwork/files/new/skewnessSummary.txt', | ||
| geneDBPath: '/app/data/metabrainnetwork/level/new/dbgenes_uint16be', | ||
| pathwayDBPath: '/app/data/metabrainnetwork/level/new/dbexternal_uint16be', | ||
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| transcriptDBpath: '/app/data/metabrainnetwork/level/new/transcriptdb', | ||
| transcriptBarsDBpath: '/app/data/metabrainnetwork/level/new/transcriptbars', | ||
| tissuecorrelationDBPath: '/app/data/metabrainnetwork/level/new/tissuedb', | ||
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| celltypeDBPath: '/app/data/metabrainnetwork/level/new/celltypedb', | ||
| correlationDBPath: '/app/data/metabrainnetwork/level/new/dbpccorrelationzscores_uint16be_genescompsstdnorm', | ||
| hpocorrelationDB: '/app/data/metabrainnetwork/level/new/hpocorrelationdb', | ||
| //correlationDBPath: '/srv/molgenis/dbpccorrelationzscores_uint16be', | ||
| requestDBPath: '/app/data/metabrainnetwork/level/new/dbreq', | ||
| networkShortURLDBPath: '/app/data/metabrainnetwork/level/new/dbnetworkurls', | ||
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| svgUploadDir: '/app/data/metabrainnetwork/uploads/svg/', | ||
| genelistUploadDir: '/app/data/metabrainnetwork/uploads/genelist', | ||
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| networkFontFamily: 'Geogrotesque Lg', | ||
| networkFontFile: 'assets/fonts/Geogtq-Lg.svg', | ||
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| useElastic: true, | ||
| elasticHost: 'elasticsearch:9200', | ||
| elasticLogLevel: 'debug', | ||
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| pubmine: { | ||
| journalFile: '/app/data/pubmine/GeneticsJournalsImpactFactorAboveThree.txt', | ||
| startYear: 2000, | ||
| stopYear: 2014, | ||
| impactFactorBins: [3, 5, 10], | ||
| numTopJournals: 5 | ||
| }, | ||
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| /*************************************************************************** | ||
| * Your SSL certificate and key, if you want to be able to serve HTTP * | ||
| * responses over https:// and/or use websockets over the wss:// protocol * | ||
| * (recommended for HTTP, strongly encouraged for WebSockets) * | ||
| * * | ||
| * In this example, we'll assume you created a folder in your project, * | ||
| * `config/ssl` and dumped your certificate/key files there: * | ||
| ***************************************************************************/ | ||
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| // ssl: { | ||
| // ca: require('fs').readFileSync(__dirname + './ssl/my_apps_ssl_gd_bundle.crt'), | ||
| // key: require('fs').readFileSync(__dirname + './ssl/my_apps_ssl.key'), | ||
| // cert: require('fs').readFileSync(__dirname + './ssl/my_apps_ssl.crt') | ||
| // }, | ||
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| /*************************************************************************** | ||
| * The `port` setting determines which TCP port your app will be * | ||
| * deployed on. * | ||
| * * | ||
| * Ports are a transport-layer concept designed to allow many different * | ||
| * networking applications run at the same time on a single computer. * | ||
| * More about ports: * | ||
| * http://en.wikipedia.org/wiki/Port_(computer_networking) * | ||
| * * | ||
| * By default, if it's set, Sails uses the `PORT` environment variable. * | ||
| * Otherwise it falls back to port 1337. * | ||
| * * | ||
| * In env/production.js, you'll probably want to change this setting * | ||
| * to 80 (http://) or 443 (https://) if you have an SSL certificate * | ||
| ***************************************************************************/ | ||
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| port: process.env.PORT || 1337, | ||
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| /*************************************************************************** | ||
| * The runtime "environment" of your Sails app is either typically * | ||
| * 'development' or 'production'. * | ||
| * * | ||
| * In development, your Sails app will go out of its way to help you * | ||
| * (for instance you will receive more descriptive error and * | ||
| * debugging output) * | ||
| * * | ||
| * In production, Sails configures itself (and its dependencies) to * | ||
| * optimize performance. You should always put your app in production mode * | ||
| * before you deploy it to a server. This helps ensure that your Sails * | ||
| * app remains stable, performant, and scalable. * | ||
| * * | ||
| * By default, Sails sets its environment using the `NODE_ENV` environment * | ||
| * variable. If NODE_ENV is not set, Sails will run in the * | ||
| * 'development' environment. * | ||
| ***************************************************************************/ | ||
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| environment: process.env.NODE_ENV || 'development', | ||
| hookTimeout: 120000 // 2 minutes | ||
| }; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| /** | ||
| * Local environment settings | ||
| * In a production environment, you probably want to leave this file out | ||
| * entirely and leave all your settings in env/production.js | ||
| */ | ||
|
|
||
| module.exports = { | ||
|
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| genesToTranscripts: '/data/genenetwork/files/genesToTranscripts.txt', | ||
| transcriptMappingFile: 'xxx', | ||
| mim2gene: '/data/genenetwork/files/new/mim2gene.txt', | ||
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| geneDescFile: '/data/genenetwork/files/new/ENSGToGeneNameHGNCBiotypeChromosomeStartStopStrandAndDescriptionV83FilteredNonChromosomesRemovedDuplicateTranscriptsRemoved.txt', | ||
| genePredScoreFile: '/data/genenetwork/files/new/skewnessSummary.txt', | ||
| geneDBPath: '/data/genenetwork/level/new/dbgenes_uint16be', | ||
| pathwayDBPath: '/data/genenetwork/level/new/dbexternal_uint16be', | ||
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| transcriptDBpath: '/data/genenetwork/level/new/transcriptdb', | ||
| transcriptBarsDBpath: '/data/genenetwork/level/new/transcriptbars', | ||
| tissuecorrelationDBPath: '/data/genenetwork/level/new/tissuedb', | ||
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| // geneDescFile: '/data/genenetwork/files/ENSGToGeneNameHGNCBiotypeChromosomeStartStopStrandAndDescriptionV75.txt.filtered.txt', | ||
| // geneDBPath: '/data/genenetwork/level/dbgenes_uint16be', | ||
| // pathwayDBPath: '/data/genenetwork/level/dbexternal_uint16be', | ||
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| celltypeDBPath: '/data/genenetwork/level/new/celltypedb', | ||
| correlationDBPath: '/data/genenetwork/level/new/dbpccorrelationzscores_uint16be_genescompsstdnorm', | ||
| hpocorrelationDB: '/data/genenetwork/level/new/hpocorrelationdb', | ||
| //correlationDBPath: '/srv/molgenis/dbpccorrelationzscores_uint16be', | ||
| requestDBPath: '/data/genenetwork/level/new/dbreq', | ||
| networkShortURLDBPath: '/data/genenetwork/level/new/dbnetworkurls', | ||
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| svgUploadDir: '/data/genenetwork/uploads/svg/', | ||
| genelistUploadDir: '/data/genenetwork/uploads/genelist', | ||
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| networkFontFamily: 'Geogrotesque Lg', | ||
| networkFontFile: 'assets/fonts/Geogtq-Lg.svg', | ||
|
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| useElastic: true, | ||
| elasticHost: 'elastichost', | ||
| elasticLogLevel: 'debug', | ||
|
|
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| pubmine: { | ||
| journalFile: '/data/pubmine/GeneticsJournalsImpactFactorAboveThree.txt', | ||
| startYear: 2000, | ||
| stopYear: 2014, | ||
| impactFactorBins: [3, 5, 10], | ||
| numTopJournals: 5 | ||
| }, | ||
|
|
||
| /*************************************************************************** | ||
| * Your SSL certificate and key, if you want to be able to serve HTTP * | ||
| * responses over https:// and/or use websockets over the wss:// protocol * | ||
| * (recommended for HTTP, strongly encouraged for WebSockets) * | ||
| * * | ||
| * In this example, we'll assume you created a folder in your project, * | ||
| * `config/ssl` and dumped your certificate/key files there: * | ||
| ***************************************************************************/ | ||
|
|
||
| // ssl: { | ||
| // ca: require('fs').readFileSync(__dirname + './ssl/my_apps_ssl_gd_bundle.crt'), | ||
| // key: require('fs').readFileSync(__dirname + './ssl/my_apps_ssl.key'), | ||
| // cert: require('fs').readFileSync(__dirname + './ssl/my_apps_ssl.crt') | ||
| // }, | ||
|
|
||
| /*************************************************************************** | ||
| * The `port` setting determines which TCP port your app will be * | ||
| * deployed on. * | ||
| * * | ||
| * Ports are a transport-layer concept designed to allow many different * | ||
| * networking applications run at the same time on a single computer. * | ||
| * More about ports: * | ||
| * http://en.wikipedia.org/wiki/Port_(computer_networking) * | ||
| * * | ||
| * By default, if it's set, Sails uses the `PORT` environment variable. * | ||
| * Otherwise it falls back to port 1337. * | ||
| * * | ||
| * In env/production.js, you'll probably want to change this setting * | ||
| * to 80 (http://) or 443 (https://) if you have an SSL certificate * | ||
| ***************************************************************************/ | ||
|
|
||
| port: process.env.PORT || 1337, | ||
|
|
||
| /*************************************************************************** | ||
| * The runtime "environment" of your Sails app is either typically * | ||
| * 'development' or 'production'. * | ||
| * * | ||
| * In development, your Sails app will go out of its way to help you * | ||
| * (for instance you will receive more descriptive error and * | ||
| * debugging output) * | ||
| * * | ||
| * In production, Sails configures itself (and its dependencies) to * | ||
| * optimize performance. You should always put your app in production mode * | ||
| * before you deploy it to a server. This helps ensure that your Sails * | ||
| * app remains stable, performant, and scalable. * | ||
| * * | ||
| * By default, Sails sets its environment using the `NODE_ENV` environment * | ||
| * variable. If NODE_ENV is not set, Sails will run in the * | ||
| * 'development' environment. * | ||
| ***************************************************************************/ | ||
|
|
||
| environment: process.env.NODE_ENV || 'development', | ||
| hookTimeout: 120000 // 2 minutes | ||
| }; |
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do not use expose in the dockerfile only specify it in the docker-compose file