Docker/Dockerfile

@@ -208,7 +208,7 @@ RUN apt-get autoclean -y && apt-get clean -y && \
 WORKDIR /usr/local/bin/
 
 # Install MHCFlurry
-RUN pip install mhcflurry
+RUN pip install mhcflurry==2.0.4
 
 ENV MHCFLURRY_DEFAULT_CLASS1_MODELS /home/neofuse/.local/share/mhcflurry/4/2.0.0
 # ENV MHCFLURRY_DEFAULT_CLASS1_MODELS /home/neofuse/.local/share/mhcflurry/4/1.6.0

Docker/source/NeoFuse_multi.sh

@@ -239,6 +239,10 @@ do
 	mkdir -p $FINALTMP
 	mkdir -p $LOGSDIR
 
+	# Create temp dir and export
+	mkdir -p $OUTDIR"/TEMPDIR/"
+	export TMPDIR=$OUTDIR"/TEMPDIR/"
+
 	# Check for PE or SE reads and process the files accordingly
 	if test -f "$READ2"; then
 		echo "[-------------------------------- [NeoFuse] --------------------------------]"
@@ -588,6 +592,7 @@ do
 	rm -rf $OUTDIRRPKM
 	rm -rf $OUTDIRCLEAVEPEP
 	rm -rf $FINALTMP
+	rm -rf $OUTDIR"/TEMPDIR/"
 	echo " The run has succesfully finished" | sed "s/^/[`date +"%T"`] /"
 	echo " All the results and log files can be found in $REALOUT/$FILE/" | sed "s/^/[`date +"%T"`] /"
 	echo "[-------------------------------- [NeoFuse] --------------------------------]"

Docker/source/NeoFuse_single.sh

@@ -209,6 +209,10 @@ mkdir -p $FINALOUTDIR
 mkdir -p $FINALTMP
 mkdir -p $LOGSDIR
 
+# Create temp dir and export
+mkdir -p $OUTDIR"/TEMPDIR/"
+export TMPDIR=$OUTDIR"/TEMPDIR/"
+
 # Check for PE or SE reads and process the files accordingly
 if test -f "$READ2"; then
 	echo "[-------------------------------- [NeoFuse] --------------------------------]"
@@ -560,6 +564,7 @@ fi
 rm -rf $OUTDIR"/FeatureCounts/"
 rm -rf $OUTDIR"/RPKM/"
 rm -rf $OUTDIR"/Peptides/"
+rm -rf $OUTDIR"/TEMPDIR/"
 echo " The run has succesfully finished" | sed "s/^/[`date +"%T"`] /"
 echo " All the results and log files can be found in $REALOUT/$FILE" | sed "s/^/[`date +"%T"`] /"
 echo "[-------------------------------- [NeoFuse] --------------------------------]"

NeoFuse

@@ -70,7 +70,7 @@ do
 done
 if [ "$BUILD" == "false" ]; then
 	if [ "$READ1" == "" ] && [ "$IN" == "" ] && [ "$BUILDREF" == "false" ] || [ "$HELP" == "true" ]; then
-		echo "NeoFuse v1.2.1
+		echo "NeoFuse v1.2.2a
 	Usage: NeoFuse <arguments> [options]
 
 	<Arguments>