From c27ac9cb52d47bb63f6b8a364e8398827682ed5a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 29 Mar 2019 15:20:09 +0100
Subject: [PATCH] hisat2: add v2.1.0

---
 apps/hisat2/.gitignore       |  1 +
 apps/hisat2/install_2.0.0.sh | 11 ++++++-----
 apps/hisat2/install_2.1.0.sh | 11 ++++++-----
 3 files changed, 13 insertions(+), 10 deletions(-)
 create mode 100644 apps/hisat2/.gitignore

diff --git a/apps/hisat2/.gitignore b/apps/hisat2/.gitignore
new file mode 100644
index 0000000..355164c
--- /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 339f196..27464f0 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 1b33c33..9c96810 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
-- 
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