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JAL-3013 resolve symlink to hmmer binaries folder
[jalview.git]
/
src
/
jalview
/
hmmer
/
HmmerCommand.java
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
f8f2cde
..
b5c1b25
100644
(file)
--- 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.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;
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
* @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);
{
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)
{
File file = FileUtils.getExecutable(cmd, binariesFolder);
if (file == null && af != null)
{