added bowtie.txt which contains the bowtie indices

SVN: 18089

openbis_contrib/source/java/ch/ethz/bsse/cisd/dsu/properties/GenomeMap.java

 package ch.ethz.bsse.cisd.dsu.properties;
+
 import java.util.HashMap;
 
 /*
@@ -18,41 +19,54 @@ import java.util.HashMap;
  */
 
 /**
- * 
- *
  * @author Manuel Kohler
  */
 
 public class GenomeMap
 {
 
-    private static String PATH_TO_GENOMES = "/array0/Genomes/"; 
-    
-    private static HashMap <String, String> genomePaths = new HashMap<String, String>();
-    
-    static {
-    genomePaths.put("PHIX", PATH_TO_GENOMES + "PhiX");
-    genomePaths.put("MUS_MUSCULUS",PATH_TO_GENOMES + "MusMus/Ncbi37_Ensembl49");
-    genomePaths.put("HOMO_SAPIENS",PATH_TO_GENOMES + "HomSap/Release36.50");
-    genomePaths.put("DROSOPHILA_MELANOGASTER",PATH_TO_GENOMES + "DrosMel/Release5");
-    genomePaths.put("CAENORHABDITIS_ELEGANS",PATH_TO_GENOMES + "Celegans/Release112708");
-    genomePaths.put("ESCHERICHIA_COLI",PATH_TO_GENOMES + "EColi");
-    genomePaths.put("RATTUS_NORVEGICUS",PATH_TO_GENOMES + "");
+    private static String PATH_TO_GENOMES = "/array0/Genomes/";
+
+    private static HashMap<String, String> genomePaths = new HashMap<String, String>();
+    static
+    {
+        genomePaths.put("PHIX", PATH_TO_GENOMES + "PhiX");
+        genomePaths.put("MUS_MUSCULUS", PATH_TO_GENOMES + "MusMus/Ncbi37_Ensembl49");
+        genomePaths.put("HOMO_SAPIENS", PATH_TO_GENOMES + "HomSap/Release36.50");
+        genomePaths.put("DROSOPHILA_MELANOGASTER", PATH_TO_GENOMES + "DrosMel/Release5");
+        genomePaths.put("CAENORHABDITIS_ELEGANS", PATH_TO_GENOMES + "Celegans/Release112708");
+        genomePaths.put("ESCHERICHIA_COLI", PATH_TO_GENOMES + "EColi");
+        genomePaths.put("RATTUS_NORVEGICUS", PATH_TO_GENOMES + "");
     }
-    
-    public static String getGenomePath(String genome) {
+
+    public static String getGenomePath(String genome)
+    {
         return genomePaths.get(genome);
     }
-    
-
-    private static HashMap <String, String> endType = new HashMap<String, String>();
 
-    static {
+    private static HashMap<String, String> endType = new HashMap<String, String>();
+    static
+    {
         endType.put("SINGLE_READ", "eland_extended");
         endType.put("PAIRED_END", "eland_pair");
-        }
-    
-        public static String getEndType(String openbisEndType) {
-            return endType.get(openbisEndType);
-        }
+    }
+
+    public static String getEndType(String openbisEndType)
+    {
+        return endType.get(openbisEndType);
+    }
+
+    private static HashMap<String, String> bowtieIndex = new HashMap<String, String>();
+    static
+    {
+        bowtieIndex.put("PHIX", "phiX");
+        bowtieIndex.put("MUS_MUSCULUS", "ncbi37_mm9");
+        bowtieIndex.put("HOMO_SAPIENS", "h_sapiens_37_asm");
+        bowtieIndex.put("DROSOPHILA_MELANOGASTER", "d_melanogaster_fb5_22");
+    }
+
+    public static String getBowtieIndex(String genome)
+    {
+        return bowtieIndex.get(genome);
+    }
 }

openbis_contrib/source/java/ch/ethz/bsse/cisd/dsu/properties/GetSampleProperties.java

@@ -48,6 +48,8 @@ public class GetSampleProperties
     private static final String END_TYPE = "END_TYPE";
 
     private static final String ELAND_CONFIG_FILE = "config.txt";
+    
+    private static final String BOWTIE_CONFIG_FILE = "bowtie.txt";
 
     private static final String DEFAULT_FLOW_CELL_SPACE = "CISD:/BSSE_FLOWCELLS/";
 //    private static final String DEFAULT_FLOW_CELL_SPACE = "default_flow_cell_space";
@@ -64,6 +66,7 @@ public class GetSampleProperties
     public static void main(String[] args) throws IOException
     {
         FileWriter writer = new FileWriter(ELAND_CONFIG_FILE);
+        FileWriter bowtieWriter = new FileWriter(BOWTIE_CONFIG_FILE);
         Properties prop = PropertyUtils.loadProperties(SERVICE_PROPERTIES);
         Long techId = 0L;
         String endType = "";
@@ -128,7 +131,9 @@ public class GetSampleProperties
         for (Entry<Integer, List<Sample>> entry : parentSamples.entrySet())
         {
             Integer key = entry.getKey();
-            String gP = "";
+            String propertyString = "";
+            String pathToGenome = "";
+            String bowtieIndexName = "";
             List<Sample> samples = entry.getValue();
             // get the properties of the first parent
             List<IEntityProperty> properties = samples.get(0).getProperties();
@@ -138,11 +143,14 @@ public class GetSampleProperties
                 {
                     try
                     {
-                        gP = GenomeMap.getGenomePath(property.tryGetAsString());
-                        if (gP != null)
+                        propertyString = property.tryGetAsString();
+                        pathToGenome = GenomeMap.getGenomePath(propertyString);
+                        bowtieIndexName = GenomeMap.getBowtieIndex(propertyString);
+                        if (pathToGenome != null)
                         {
-                            writer.write(key + ":ELAND_GENOME " + gP + "\n");
+                            writer.write(key + ":ELAND_GENOME " + pathToGenome + "\n");
                             writer.write(key + ":ANALYSIS " + endType + "\n");
+                            bowtieWriter.write(bowtieIndexName + "\n");
                         }
 
                     } catch (IOException ex)
@@ -154,7 +162,9 @@ public class GetSampleProperties
         }
         writer.write("ELAND_SET_SIZE 10\n" + "EMAIL_LIST manuel.kohler@bsse.ethz.ch");
         writer.close();
+        bowtieWriter.close();
         operationLog.info("Writing " + ELAND_CONFIG_FILE);
+        operationLog.info("Writing " + BOWTIE_CONFIG_FILE);
         service.logout(sessionToken);
     }