X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FMafftWS.java;fp=webservices%2Fcompbio%2Fws%2Fserver%2FMafftWS.java;h=12805af17e733a0061ffe77c798c9dd73476facf;hb=61af8ce2cea02220228f58b30b4319f500b2f040;hp=eda824a5759c03c48b6d9595fc7c70cd6d5e17dc;hpb=603a6be6b9459625f535bf42c6d8ec5462e218e2;p=jabaws.git

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index eda824a..12805af 100644
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -31,6 +31,7 @@ import compbio.data.sequence.FastaSequence;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -70,6 +71,9 @@ public class MafftWS implements MsaWS<Mafft> {
 	ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
 			throws JobSubmissionException {
 		Mafft mafft = new Mafft();
+		mafft.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
 		return Configurator.configureExecutable(mafft, dataSet);
 	}