Description: Alter the launching script, the config file and relevant Java
 files for a Debian install:
 - Simplify the paths to account for a Debian installation.
 - Use the default /etc/snpeff/snpEff.config file as configuration file if no
  file was given in the command line: it will be copied into
  ~/.snpEff/snpEff.config, which will be used as the configuration file is no
  other is given on the command line.
 - By default, put data in ~/.snpEff/data.
 - Correct bashisms in the launching script.
 - In Config.java, use per-user config file if available. Else use the file in
  /etc/snpeff. Else (which should normally just concern the unit tests), use
  default file which should be in the source tree.
 - Indicate path to effective config file in Java files.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2022-02-07

--- a/scripts/snpEff
+++ b/scripts/snpEff
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 #---------------------------------------------------------------------------------------------------
 #
@@ -13,13 +13,7 @@
 # Created by: Brad Chapman
 #---------------------------------------------------------------------------------------------------
 
-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
-
-java=java
-if [ -e "$JAVA_HOME/bin/java" ]
-then
-	java="$JAVA_HOME/bin/java"
-fi
+jardir=/usr/share/java
 
 default_jvm_mem_opts="-Xms1g -Xmx8g"
 jvm_mem_opts=""
@@ -39,12 +33,20 @@
     esac
 done
 
-if [ "$jvm_mem_opts" == "" ]; then
+if [ "$jvm_mem_opts" = "" ]; then
     jvm_mem_opts="$default_jvm_mem_opts"
 fi
-if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then
-    pass_args="$pass_args -c ${jardir}/snpEff.config"
+if [ "$pass_args" != "" ] && ! echo "$pass_args" | grep "\-c " ; then
+    if [ ! -d ~/.snpEff ]; then
+        mkdir ~/.snpEff
+    fi
+
+    if [ -d ~/.snpEff -a ! -e ~/.snpEff/snpEff.config ]; then
+        cp /etc/snpeff/snpEff.config ~/.snpEff/snpEff.config
+    fi
+
+    pass_args="$pass_args -c $HOME/.snpEff/snpEff.config"
 fi
 
-exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args
+exec java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpeff.jar $pass_args
 exit
--- a/config/snpEff.config
+++ b/config/snpEff.config
@@ -18,7 +18,7 @@
 # Also, a non-absolute path will be relative to config's file dir
 # 
 #---
-data.dir = ./data/
+data.dir = ~/.snpEff/data/
 
 #---
 # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')
--- a/src/main/java/org/snpeff/PromoterSequences.java
+++ b/src/main/java/org/snpeff/PromoterSequences.java
@@ -63,7 +63,7 @@
 		genes = new HashSet<Gene>();
 
 		Log.info("Loading database");
-		String configFile = HOME + "/snpEff/snpEff.config";
+		String configFile = HOME + "/.snpEff/snpEff.config";
 		config = new Config(genomeName, configFile);
 		config.loadSnpEffectPredictor();
 		snpEffectPredictor = config.getSnpEffectPredictor();
--- a/src/main/java/org/snpeff/SnpEff.java
+++ b/src/main/java/org/snpeff/SnpEff.java
@@ -167,7 +167,7 @@
 
 	public SnpEff() {
 		genomeVer = ""; // Genome version
-		configFile = Config.DEFAULT_CONFIG_FILE; // Config file
+		configFile = Config.defaultConfigFile(); // Config file
 		verbose = false; // Be verbose
 		debug = false; // Debug mode
 		quiet = false; // Be quiet
--- a/src/main/java/org/snpeff/snpEffect/Config.java
+++ b/src/main/java/org/snpeff/snpEffect/Config.java
@@ -16,6 +16,8 @@
 public class Config implements Serializable, Iterable<String> {
 
     public static final String DEFAULT_CONFIG_FILE = "snpEff.config";
+    public static final String ETC_CONFIG_FILE = "/etc/snpeff/snpEff.config";
+    public static final String PREFERRED_CONFIG_FILE = Gpr.HOME + "/.snpEff/snpEff.config";
     public static final String DEFAULT_DATA_DIR = "./data";
     // Keys in properties file
     public static final String KEY_BUNDLE_SUFIX = ".bundle";
@@ -98,7 +100,7 @@
      * Create a config (uses DEFAULT_CONFIG_FILE)
      */
     public Config(String genomeVersion) {
-        init(genomeVersion, DEFAULT_CONFIG_FILE, null, null);
+        init(genomeVersion, defaultConfigFile(), null, null);
     }
 
     /**
@@ -201,6 +203,23 @@
         }
     }
 
+    /**
+     * If Debian-preferred config file is available, give it.
+     * else, if the config file in /etc/snpeff is available, give it.
+     * Else, default to DEFAULT_CONFIG_FILE.
+     */
+    public static String defaultConfigFile() {
+        File preferred = new File(PREFERRED_CONFIG_FILE);
+        File etcFile = new File(ETC_CONFIG_FILE);
+        if (preferred.exists()) {
+            return PREFERRED_CONFIG_FILE;
+        } else if (etcFile.exists()) {
+            return ETC_CONFIG_FILE;
+        } else {
+            return DEFAULT_CONFIG_FILE;
+        }
+    }
+
     /**
      * Get a list of URLs that can be used to download a database
      * Use compatible versions from 'getDatabaseCompatibilityVersions()'
--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java
+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java
@@ -47,7 +47,7 @@
 	int totalOk = 0;
 	int totalWarnings = 0;
 	int totalNotFound = 0;
-	String configFile = Config.DEFAULT_CONFIG_FILE;
+	String configFile = Config.defaultConfigFile();
 	String proteinFile = "";
 	Map<String, String> proteinById; // Protein sequence by ID (transcript ID, protein ID, etc.)
 	AutoHashMap<String, List<Transcript>> trByChromo;
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
@@ -37,13 +37,13 @@
 		genomeName = "test";
 		this.verbose = verbose;
 		this.snpEffectPredictor = snpEffectPredictor;
-		config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
+		config = new Config("testCase", Config.defaultConfigFile());
 	}
 
 	public CompareEffects(String genomeName, boolean verbose) {
 		this.genomeName = genomeName;
 		this.verbose = verbose;
-		config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
+		config = new Config("testCase", Config.defaultConfigFile());
 	}
 
 	/**
@@ -113,7 +113,7 @@
 
 	public void initSnpEffPredictor() {
 		// Create a config and force out snpPredictor for hg37 chromosome Y
-		config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
+		config = new Config(genomeName, Config.defaultConfigFile());
 
 		if (snpEffectPredictor == null) {
 			config.loadSnpEffectPredictor();
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
@@ -57,7 +57,7 @@
 	public CompareToEnsembl(String genomeName, boolean throwException) {
 		this.throwException = throwException;
 		if (verbose) Log.info("Loading predictor");
-		config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
+		config = new Config(genomeName, Config.defaultConfigFile());
 		config.loadSnpEffectPredictor();
 		snpEffectPredictor = config.getSnpEffectPredictor();
 		genome = config.getGenome();
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
@@ -33,7 +33,7 @@
 	 */
 	public void run() {
 		Log.debug("Loading config files");
-		Config config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
+		Config config = new Config("testCase", Config.defaultConfigFile());
 		config.loadSnpEffectPredictor();
 
 		for (Gene gint : config.getGenome().getGenes()) {
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
@@ -75,7 +75,7 @@
      */
     protected void initSnpEffPredictor(boolean addUtrs, boolean onlyPlusStrand) {
         // Create a config and force out snpPredictor for hg37 chromosome Y
-        if (config == null) config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
+        if (config == null) config = new Config("testCase", Config.defaultConfigFile());
 
         // Initialize factory
         int maxGeneLen = 1000;
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
@@ -95,7 +95,7 @@
         String expectedResult = Gpr.readFile(resultFile).trim();
 
         // Build
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryRefSeq factory = new SnpEffPredictorFactoryRefSeq(config);
         factory.setFileName(refSeqFile);
         factory.setVerbose(verbose);
@@ -118,7 +118,7 @@
      * Build a genome from a embl file and compare results to 'expected' results
      */
     public SnpEffectPredictor buildEmbl(String genome, String emblFile) {
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryEmbl sepEmbl = new SnpEffPredictorFactoryEmbl(config, emblFile);
         SnpEffectPredictor sep = sepEmbl.create();
         return sep;
@@ -132,7 +132,7 @@
      * Build a genome from a genbank file and compare results to 'expected' results
      */
     public SnpEffectPredictor buildGeneBank(String genome, String genBankFile, boolean circularCorrectlargeGap) {
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryGenBank sepfg = new SnpEffPredictorFactoryGenBank(config, genBankFile);
         sepfg.setVerbose(verbose);
         sepfg.setCircularCorrectLargeGap(circularCorrectlargeGap);
@@ -157,7 +157,7 @@
      */
     public SnpEffectPredictor buildGff3AndCompare(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) {
         // Build
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryGff3 fgff3 = new SnpEffPredictorFactoryGff3(config);
         fgff3.setVerbose(verbose);
         if (gff3File != null) fgff3.setFileName(gff3File);
@@ -194,7 +194,7 @@
         String expectedResult = Gpr.readFile(resultFile).trim();
 
         // Build
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);
         fgtf22.setFileName(gtf22);
         fgtf22.setVerbose(verbose);
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
@@ -50,7 +50,7 @@
         //---
         // Load database and check some numbers
         //---
-        String configFile = Config.DEFAULT_CONFIG_FILE;
+        String configFile = Config.defaultConfigFile();
         Config config = new Config(genomeName, configFile);
         if (verbose) Log.info("Loading database");
         SnpEffectPredictor snpEffectPredictor = config.loadSnpEffectPredictor();
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
@@ -281,7 +281,7 @@
 
 		// Load database
 		String genomeVer = "testHg3766Chr1";
-		config = new Config(genomeVer, Config.DEFAULT_CONFIG_FILE);
+		config = new Config(genomeVer, Config.defaultConfigFile());
 		config.loadSnpEffectPredictor();
 		config.setTreatAllAsProteinCoding(true); // For historical reasons...
 		config.getSnpEffectPredictor().buildForest();
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
@@ -25,7 +25,7 @@
         // Load database
         String genomeVer = "testHg3766Chr1";
         Log.debug("Loading database '" + genomeVer + "'");
-        Config config = new Config(genomeVer, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genomeVer, Config.defaultConfigFile());
         config.setTreatAllAsProteinCoding(true); // For historical reasons...
         config.loadSnpEffectPredictor();
 
--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
@@ -225,7 +225,7 @@
     @Test
     public void test_25_exon_bases() {
         Log.debug("Test");
-        Config config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config("testCase", Config.defaultConfigFile());
         config.loadSnpEffectPredictor();
 
         String fastaFile = path("testCase.fa");
@@ -283,7 +283,7 @@
         String gtfFile = path("ENSMUSG00000005763.gtf");
         String genome = "testMm37.61";
 
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);
         fgtf22.setFileName(gtfFile);
         fgtf22.setReadSequences(false); // Don't read sequences
--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
@@ -254,7 +254,7 @@
     protected void initSnpEffPredictor(Gene[] genesToAdd) {
         // Create a config and force out snpPredictor
         if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {
-            config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
+            config = new Config(genomeName, Config.defaultConfigFile());
         }
 
         // Initialize factory
--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
@@ -44,7 +44,7 @@
     protected void initSnpEffPredictor() {
         // Create a config and force out snpPredictor
         if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {
-            config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
+            config = new Config(genomeName, Config.defaultConfigFile());
         }
 
         // Create predictor
--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
@@ -30,7 +30,7 @@
         };
 
         // Build
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryGff3 sefGff = new SnpEffPredictorFactoryGff3(config);
         sefGff.setFileName(gff);
         sefGff.setVerbose(verbose);
@@ -68,7 +68,7 @@
         };
 
         // Build
-        Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+        Config config = new Config(genome, Config.defaultConfigFile());
         SnpEffPredictorFactoryGff3 sefGff = new SnpEffPredictorFactoryGff3(config);
         sefGff.setFileName(gff);
         sefGff.setFastaFile(fasta);