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* app module is now used for CLI. Classes and options created * log4j is now used instead of 'simple' and log4j.properties created in resources * core module package renamed
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#!/bin/bash | ||
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if [ $# -eq 1 ]; then | ||
if [ $1 == 'run-maven' ]; then | ||
mvn clean install -DskipTests | ||
fi | ||
fi | ||
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## Check if 'build' folder exists to delete the content. If not it is created. | ||
if [ -d build ]; then | ||
rm -rf build/* | ||
else | ||
mkdir build | ||
fi | ||
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## Copy all the binaries, dependencies and files | ||
cp -r hpg-bigdata-app/target/appassembler/* build/ | ||
cp README.md build/ | ||
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62 changes: 62 additions & 0 deletions
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hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/BigDataMain.java
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package org.opencb.hpg.bigdata.app; | ||
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import org.opencb.hpg.bigdata.app.cli.*; | ||
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/** | ||
* Created by imedina on 15/03/15. | ||
*/ | ||
public class BigDataMain { | ||
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public static void main(String[] args) { | ||
CliOptionsParser cliOptionsParser = new CliOptionsParser(); | ||
cliOptionsParser.parse(args); | ||
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String parsedCommand = cliOptionsParser.getCommand(); | ||
if (parsedCommand == null || parsedCommand.isEmpty()) { | ||
if (cliOptionsParser.getGeneralOptions().help) { | ||
cliOptionsParser.printUsage(); | ||
} | ||
if (cliOptionsParser.getGeneralOptions().version) { | ||
System.out.println("version = 3.1.0"); | ||
} | ||
} else { | ||
CommandExecutor commandExecutor = null; | ||
switch (parsedCommand) { | ||
case "fastq": | ||
if (cliOptionsParser.getFastqCommandOptions().commonOptions.help) { | ||
cliOptionsParser.printUsage(); | ||
} else { | ||
commandExecutor = new FastqCommandExecutor(cliOptionsParser.getFastqCommandOptions()); | ||
} | ||
break; | ||
case "bam": | ||
if (cliOptionsParser.getBamCommandOptions().commonOptions.help) { | ||
cliOptionsParser.printUsage(); | ||
} else { | ||
commandExecutor = new BamCommandExecutor(cliOptionsParser.getBamCommandOptions()); | ||
} | ||
break; | ||
case "ga4gh": | ||
if (cliOptionsParser.getGa4ghCommandOptions().commonOptions.help) { | ||
cliOptionsParser.printUsage(); | ||
} else { | ||
commandExecutor = new Ga4ghCommandExecutor(cliOptionsParser.getGa4ghCommandOptions()); | ||
} | ||
break; | ||
case "align": | ||
if (cliOptionsParser.getAlignCommandOptions().commonOptions.help) { | ||
cliOptionsParser.printUsage(); | ||
} else { | ||
commandExecutor = new AlignCommandExecutor(cliOptionsParser.getAlignCommandOptions()); | ||
} | ||
break; | ||
default: | ||
break; | ||
} | ||
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if (commandExecutor != null) { | ||
commandExecutor.parse(); | ||
} | ||
} | ||
} | ||
} |
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hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/AlignCommandExecutor.java
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package org.opencb.hpg.bigdata.app.cli; | ||
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/** | ||
* Created by imedina on 16/03/15. | ||
*/ | ||
public class AlignCommandExecutor extends CommandExecutor { | ||
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private CliOptionsParser.AlignCommandOptions alignCommandOptions; | ||
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public AlignCommandExecutor(CliOptionsParser.AlignCommandOptions alignCommandOptions) { | ||
super(alignCommandOptions.commonOptions.logLevel, alignCommandOptions.commonOptions.verbose, | ||
alignCommandOptions.commonOptions.conf); | ||
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this.alignCommandOptions = alignCommandOptions; | ||
} | ||
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/** | ||
* Parse specific 'align' command options | ||
*/ | ||
public void parse() { | ||
logger.info("Executing {} CLI options", "align"); | ||
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logger.debug("Input file: {}", alignCommandOptions.input); | ||
} | ||
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} |
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hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/BamCommandExecutor.java
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package org.opencb.hpg.bigdata.app.cli; | ||
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/** | ||
* Created by imedina on 15/03/15. | ||
*/ | ||
public class BamCommandExecutor extends CommandExecutor { | ||
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private CliOptionsParser.BamCommandOptions bamCommandOptions; | ||
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public BamCommandExecutor(CliOptionsParser.BamCommandOptions bamCommandOptions) { | ||
super(bamCommandOptions.commonOptions.logLevel, bamCommandOptions.commonOptions.verbose, | ||
bamCommandOptions.commonOptions.conf); | ||
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this.bamCommandOptions = bamCommandOptions; | ||
} | ||
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/** | ||
* Parse specific 'bam' command options | ||
*/ | ||
public void parse() { | ||
logger.info("Executing {} CLI options", "bam"); | ||
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logger.debug("Input file: {}", bamCommandOptions.input); | ||
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} | ||
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} |
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