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R issue in Queue fixed. 

GSA-721
This commit is contained in:
Tad Jordan 2013-01-28 11:33:49 -05:00
parent aab160372a
commit 8777e02aa5
2 changed files with 12 additions and 4 deletions
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10
public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
View File

@ -110,15 +110,17 @@ public class RScriptExecutor {
List<File> tempFiles = new ArrayList<File>(); List<File> tempFiles = new ArrayList<File>();
try { try {
File tempLibDir = IOUtils.tempDir("Rlib.", ""); File tempLibSourceDir = IOUtils.tempDir("RlibSources.", "");
tempFiles.add(tempLibDir); File tempLibInstallationDir = IOUtils.tempDir("Rlib.", "");
tempFiles.add(tempLibSourceDir);
tempFiles.add(tempLibInstallationDir);
StringBuilder expression = new StringBuilder("tempLibDir = '").append(tempLibDir).append("';"); StringBuilder expression = new StringBuilder("tempLibDir = '").append(tempLibInstallationDir).append("';");
if (this.libraries.size() > 0) { if (this.libraries.size() > 0) {
List<String> tempLibraryPaths = new ArrayList<String>(); List<String> tempLibraryPaths = new ArrayList<String>();
for (RScriptLibrary library: this.libraries) { for (RScriptLibrary library: this.libraries) {
File tempLibrary = library.writeTemp(); File tempLibrary = library.writeLibrary(tempLibSourceDir);
tempFiles.add(tempLibrary); tempFiles.add(tempLibrary);
tempLibraryPaths.add(tempLibrary.getAbsolutePath()); tempLibraryPaths.add(tempLibrary.getAbsolutePath());
} }

6
public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java
View File

@ -57,4 +57,10 @@ public enum RScriptLibrary {
public File writeTemp() { public File writeTemp() {
return IOUtils.writeTempResource(new Resource(getResourcePath(), RScriptLibrary.class)); return IOUtils.writeTempResource(new Resource(getResourcePath(), RScriptLibrary.class));
} }
public File writeLibrary(File tempDir) {
File libraryFile = new File(tempDir, getLibraryName());
IOUtils.writeResource(new Resource(getResourcePath(), RScriptLibrary.class), libraryFile);
return libraryFile;
}
} }