bbmap to 37.90

2 files changed, 23 insertions, 24 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 1a84c71a5a57..22e9f242333f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,15 +1,15 @@
 pkgbase = bbmap
-	pkgdesc = A short read aligner, and other bioinformatic tools
-	pkgver = 37.62
+	pkgdesc = A short read aligner2 and other bioinformatic tools
+	pkgver = 37.90
 	pkgrel = 1
-	url = http://jgi.doe.gov/data-and-tools/bbtools/
+	url = https://jgi.doe.gov/data-and-tools/bbtools/
 	arch = x86_64
 	license = BSD
 	depends = env-modules
 	depends = jre8-openjdk>=7
 	optdepends = samtools: for BAM output
-	source = https://downloads.sourceforge.net/project/bbmap/BBMap_37.62.tar.gz
-	md5sums = e67f0f359550e3d158bba7b07c15b702
+	source = https://downloads.sourceforge.net/project/bbmap/BBMap_37.90.tar.gz
+	sha256sums = f2df007b581aec1b4278e2c115f52afef2bb3e4117c1cd5bd11bbf4993d10bbe
 
 pkgname = bbmap
 
diff --git a/PKGBUILD b/PKGBUILD
index 09e798199f29..3692092c45f0 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,40 +1,39 @@
 # Maintainer: Clint Valentine <valentine.clint@gmail.com>
 
 pkgname=bbmap
-pkgver=37.62
+pkgver=37.90
 pkgrel=1
-pkgdesc="A short read aligner, and other bioinformatic tools"
+pkgdesc="A short read aligner2 and other bioinformatic tools"
 arch=('x86_64')
-url="http://jgi.doe.gov/data-and-tools/bbtools/"
+url=https://jgi.doe.gov/data-and-tools/bbtools/
 license=('BSD')
 depends=('env-modules' 'jre8-openjdk>=7')
 optdepends=('samtools: for BAM output')
-source=("https://downloads.sourceforge.net/project/${pkgname}/BBMap_${pkgver}.tar.gz")
-md5sums=('e67f0f359550e3d158bba7b07c15b702')
+source=(https://downloads.sourceforge.net/project/"${pkgname}"/BBMap_"${pkgver}".tar.gz)
+sha256sums=('f2df007b581aec1b4278e2c115f52afef2bb3e4117c1cd5bd11bbf4993d10bbe')
 
 build() {
-  cd "${srcdir}/${pkgname}/jni"
+  cd "${srcdir}"/"${pkgname}"/jni
   #make -f makefile.linux  # No jni.h found?
 }
 
 package() {
-  cd "${srcdir}/${pkgname}"
+  cd "${srcdir}"/"${pkgname}"
 
-  mkdir -p "${pkgdir}/usr/share/doc/${pkgname}/"
-  cp -r docs/* "${pkgdir}/usr/share/doc/${pkgname}/"
-
-  mkdir -p "${pkgdir}/usr/share/java/${pkgname}/"
-  cp -r config "${pkgdir}/usr/share/java/${pkgname}/"
-  cp -r current "${pkgdir}/usr/share/java/${pkgname}/"
-  cp -r jni "${pkgdir}/usr/share/java/${pkgname}/"
-  cp -r pipelines "${pkgdir}/usr/share/java/${pkgname}/"
-  cp -r resources "${pkgdir}/usr/share/java/${pkgname}/"
+  mkdir -p "${pkgdir}"/usr/share/doc/"${pkgname}"/
+  cp -r docs/* "${pkgdir}"/usr/share/doc/"${pkgname}"/
 
+  mkdir -p "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r config "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r current "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r jni "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r pipelines "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r resources "${pkgdir}"/usr/share/java/"${pkgname}"/
 
   for script in *.sh; do
-    sed -i "s#CP=.*#CP=/usr/share/java/${pkgname}/current/#" "${script}"
-    sed -i "s#DIR=.*#DIR=/usr/share/java/${pkgname}/#" "${script}"
+    sed -i s#'CP=.*'#CP=/usr/share/java/"${pkgname}"/current/# "${script}"
+    sed -i s#'DIR=.*'#DIR=/usr/share/java/"${pkgname}"/# "${script}"
 
-    install -Dm775 "${script}" "${pkgdir}/usr/bin/${script}"
+    install -Dm775 "${script}" "${pkgdir}"/usr/bin/"${script}"
   done
 }