diff --git a/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java b/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java index b39f1411..a4ef0dea 100644 --- a/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java +++ b/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java @@ -15,9 +15,11 @@ public class VariantRvTestsCLITest { Path confPath; private void init() throws URISyntaxException { - inPath = Paths.get("/home/jtarraga/data/vcf/skat/example.vcf.avro"); - outPath = Paths.get("/home/jtarraga/data/vcf/skat/out"); - confPath = Paths.get("/home/jtarraga/data/vcf/skat/skat.params"); + String root = "/home/jtarraga/data100/vcf/rvtest-skat/spark"; +// String root = "/home/jtarraga/data/vcf/skat/"; + inPath = Paths.get(root + "/example.vcf.avro"); + outPath = Paths.get(root + "/out"); + confPath = Paths.get(root + "/skat.params"); } // @Test diff --git a/hpg-bigdata-tools/src/main/java/org/opencb/hpg/bigdata/tools/variant/analysis/RvTestsAnalysis.java b/hpg-bigdata-tools/src/main/java/org/opencb/hpg/bigdata/tools/variant/analysis/RvTestsAnalysis.java index f3e546ac..80d9c9e3 100644 --- a/hpg-bigdata-tools/src/main/java/org/opencb/hpg/bigdata/tools/variant/analysis/RvTestsAnalysis.java +++ b/hpg-bigdata-tools/src/main/java/org/opencb/hpg/bigdata/tools/variant/analysis/RvTestsAnalysis.java @@ -26,9 +26,9 @@ public class RvTestsAnalysis { private String outDirname; private String confFilename; - private final String RVTEST_BIN = "/home/jtarraga/softs/rvtests/executable/rvtest"; - private final String BGZIP_BIN = "/home/joaquin/softs/htslib/bgzip"; - private final String TABIX_BIN = "/home/joaquin/softs/htslib/tabix"; + private final String RVTEST_BIN = "/home/jtarraga/soft/rvtests/executable/rvtest"; + private final String BGZIP_BIN = "/usr/bin/bgzip"; //"/home/joaquin/softs/htslib/bgzip"; + private final String TABIX_BIN = "/usr/bin/tabix"; //"/home/joaquin/softs/htslib/tabix"; public RvTestsAnalysis(String inFilename, String outDirname, String confFilename) { this.inFilename = inFilename;