diff --git a/apps/hisat2/.gitignore b/apps/hisat2/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e
--- /dev/null
+++ b/apps/hisat2/.gitignore
@@ -0,0 +1 @@
+*/
diff --git a/apps/hisat2/install_2.0.0.sh b/apps/hisat2/install_2.0.0.sh
index 339f196dcbf903ba89e946b61a45e1dfcddb71c6..27464f037e7f608795643738b46dc06e54b45b88 100644
--- a/apps/hisat2/install_2.0.0.sh
+++ b/apps/hisat2/install_2.0.0.sh
@@ -36,12 +36,13 @@
 source ../build_env.sh
 
 HISAT2_VERSION=2.0.0
-curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip 
-unzip hisat2_linux-v${HISAT2_VERSION}.zip 
+curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip
+unzip hisat2_linux-v${HISAT2_VERSION}.zip
 mkdir ${HISAT2_VERSION}
 mkdir ${HISAT2_VERSION}/bin
-cd hisat2-${HISAT2_VERSION}-beta 
-make 
+cd hisat2-${HISAT2_VERSION}-beta
+make
 cp hisat2 ../${HISAT2_VERSION}/bin && \
 cp hisat2-* ../${HISAT2_VERSION}/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}-beta 
+rm -Rf hisat2-${HISAT2_VERSION}-beta
+rm -Rf hisat2-${HISAT2_VERSION}-beta.zip
diff --git a/apps/hisat2/install_2.1.0.sh b/apps/hisat2/install_2.1.0.sh
index 1b33c33033ede71362b6b8d74e94120cd1ea79d7..9c968108d44dfb6ed565f2ba37e653a34b89b4e4 100644
--- a/apps/hisat2/install_2.1.0.sh
+++ b/apps/hisat2/install_2.1.0.sh
@@ -36,12 +36,13 @@
 source ../build_env.sh
 
 HISAT2_VERSION=2.1.0
-curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip 
-unzip hisat2_linux-v${HISAT2_VERSION}.zip 
+curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${HISAT2_VERSION}-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip
+unzip hisat2_linux-v${HISAT2_VERSION}.zip
 mkdir ${HISAT2_VERSION}
 mkdir ${HISAT2_VERSION}/bin
-cd hisat2-${HISAT2_VERSION}-beta 
-make 
+cd hisat2-${HISAT2_VERSION}
+make
 cp hisat2 ../${HISAT2_VERSION}/bin && \
 cp hisat2-* ../${HISAT2_VERSION}/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}-beta 
+rm -Rf hisat2-${HISAT2_VERSION}
+rm -Rf hisat2-${HISAT2_VERSION}.zip