app: get the RvTest binary path from the command line #125

opencb · Sep 18, 2017 · 360b56d · 360b56d
1 parent 832c5a0
commit 360b56d
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Showing 5 changed files with 14 additions and 14 deletions.
diff --git a/...alysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java b/...alysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java
@@ -40,9 +40,9 @@ public RvTestsWrapper(String studyId, String inFilename, String metaFilename,
     public void execute() throws AnalysisExecutorException {
         // Sanity chek
         if (binPath == null || !binPath.toFile().exists()) {
-            String msg = "RvTests binary path is missing.";
-            logger.error("RvTests binary path is missing.");
-            throw new AnalysisExecutorException("RvTests binary path is missing.");
+            String msg = "RvTests binary path is missing or does not exist:  '" + binPath + "'.";
+            logger.error(msg);
+            throw new AnalysisExecutorException(msg);
         }
 
         // Get output dir

diff --git a/.../src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java b/.../src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java
@@ -412,8 +412,12 @@ public void rvtests() throws Exception {
                 variantCommandOptions.rvtestsVariantCommandOptions.filterParameters,
                 variantCommandOptions.rvtestsVariantCommandOptions.rvtestsParams);
 
-        // TODO: get the binary path from config folder
-        rvtests.setBinPath(Paths.get("/home/jtarraga/soft/rvtests/executable/rvtest"));
+        // Get the binary path from input parameter
+        String binPath = variantCommandOptions.rvtestsVariantCommandOptions.binPath;
+        if (StringUtils.isEmpty(binPath)) {
+            binPath = "rvtest";
+        }
+        rvtests.setBinPath(Paths.get(binPath));
         rvtests.execute();
     }
 }
diff --git a/...app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java b/...app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
@@ -357,17 +357,11 @@ public class RvTestsVariantCommandOptions {
         @Parameter(names = {"-i", "--input"}, description = "Input file name (in Avro/Parquet file format).",
                 required = true, arity = 1)
         public String inFilename;
-/*
-        @Parameter(names = {"-m", "--metadata"}, description = "Input metadata file name.",
-                required = true, arity = 1)
-        public String metaFilename;
-
-        @Parameter(names = {"-o", "--output"}, description = "Output directory name to save the rvtests results.",
-                required = true, arity = 1)
-        public String outDirname;
 
-*/
         @DynamicParameter(names = "-D", description = "RvTests parameters")
         public Map<String, String> rvtestsParams = new HashMap<>();
+
+        @Parameter(names = {"--rvtest-path"}, description = "Path to the RvTest executable.", arity = 1)
+        public String binPath = null;
     }
 }
diff --git a/...bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java b/...bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java
@@ -57,6 +57,7 @@ public void skat() {
             commandLine.append(" variant rvtests");
             commandLine.append(" --log-level ERROR");
             commandLine.append(" --dataset ").append(datasetName);
+            commandLine.append(" --rvtest-path ../../../soft/rvtests/executable/rvtest");
             commandLine.append(" -i ").append(avroPath);
             commandLine.append(" -Dsingle=wald");
             commandLine.append(" -Dout=/tmp/out.wald");

diff --git a/hpg-bigdata-app/src/test/resources/example.vcf b/hpg-bigdata-app/src/test/resources/example.vcf
@@ -3,6 +3,7 @@
 ##fileDate=20140730
 ##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
 ##source=1000GenomesPhase3Pipeline
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	P1	P2	P3	P4	P5	P6	P7	P8	P9
 1	1	.	A	G	100	.	.	GT	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0
 1	2	.	A	G	100	.	.	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1