initial hisat2 download and bundling

.gitignore

@@ -22,6 +22,7 @@ forDist/FastQC/**
 forDist/linux/samtools
 forDist/win32/*.exe
 forDist/bootstrap.min.css
+forDist/hisat2*
 src/installUpdateProcess/*.dll
 \.idea/
 src/**/*.js

scripts/install/getHisat2.bash

@@ -0,0 +1,24 @@
+(set -o igncr) 2>/dev/null && set -o igncr; # For Cygwin on Windows compaibility
+
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    wget "http://ccb.jhu.edu/software/hisat2/dl/hisat2-2.1.0-Linux_x86_64.zip"
+
+    unzip hisat2-2.1.0-Linux_x86_64.zip
+
+    cp hisat2-2.1.0/hisat2 forDist
+    cp hisat2-2.1.0//hisat2-build forDist
+    cp hisat2-2.1.0/hisat2-build-s forDist
+    cp hisat2-2.1.0/hisat2-build-l forDist
+    cp hisat2-2.1.0/hisat2-align-s forDist
+    cp hisat2-2.1.0/hisat2-align-l forDist
+    cp hisat2-2.1.0/hisat2-inspect forDist
+    cp hisat2-2.1.0/hisat2-inspect-s forDist
+    cp hisat2-2.1.0/hisat2-inspect-l forDist
+
+    rm hisat2-2.1.0-Linux_x86_64.zip
+    rm -rf hisat2-2.1.0
+fi
+
+if [[ "$OSTYPE" == "cygwin" ]]; then
+	wget "http://www.di.fc.ul.pt/~afalcao/hisat2.1/hisat2.1_Windows.zip"
+fi