From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 6 Jun 2018 14:33:26 +0000 (+0100)
Subject: JAL-3013 resolve symlink to hmmer binaries folder
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e0fd9965a1ffacf4ac034a79e7cb5f7e898ff69f;p=jalview.git

JAL-3013 resolve symlink to hmmer binaries folder
---

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index f8f2cde..b5c1b25 100644
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -24,6 +24,7 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -247,10 +248,13 @@ public abstract class HmmerCommand implements Runnable
    * @param cmd
    *          command short name e.g. hmmalign
    * @return
+   * @throws IOException
    */
-  protected String getCommandPath(String cmd)
+  protected String getCommandPath(String cmd) throws IOException
   {
     String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
+    // ensure any symlink to the directory is resolved:
+    binariesFolder = Paths.get(binariesFolder).toRealPath().toString();
     File file = FileUtils.getExecutable(cmd, binariesFolder);
     if (file == null && af != null)
     {