First commit with PKGBUILD, .SRCINFO, and bash wrapper

3 files changed, 67 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..e1af2e019d8f
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,20 @@
+pkgbase = fgbio-git
+	pkgdesc = Tools for working with genomic and high throughput sequencing data.
+	pkgver = 0.4.0.r19.g4ba4127
+	pkgrel = 1
+	url = https://github.com/fulcrumgenomics/fgbio
+	arch = any
+	license = MIT
+	checkdepends = r
+	checkdepends = r-cran-ggplot2
+	depends = git-lfs
+	depends = java-runtime>=8
+	depends = sbt
+	depends = scala>=2.12
+	provides = fgbio
+	conflicts = fgbio
+	source = fgbio.sh
+	md5sums = 8f3581b03a37ecaf0824f5c38b2c4f19
+
+pkgname = fgbio-git
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..d9ae2b5711cf
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,45 @@
+# Maintainer: Clint Valentine <valentine.clint@gmail.com>
+
+pkgname=fgbio-git
+pkgver=0.4.0.r19.g4ba4127
+pkgrel=1
+pkgdesc="Tools for working with genomic and high throughput sequencing data."
+arch=('any')
+url="https://github.com/fulcrumgenomics/fgbio"
+license=('MIT')
+depends=('git-lfs' 'java-runtime>=8' 'sbt' 'scala>=2.12')
+checkdepends=('r' 'r-cran-ggplot2')
+provides=('fgbio')
+conflicts=('fgbio')
+source=("fgbio.sh")
+md5sums=("8f3581b03a37ecaf0824f5c38b2c4f19")
+
+prepare() {
+  # Git LFS fails when used as a 'source'
+  if [[ -d fgbio ]]; then cd fgbio && git pull; else git clone https://github.com/fulcrumgenomics/fgbio.git; fi
+}
+
+pkgver() {
+  cd "fgbio"
+  git describe --long --tags | sed 's/\([^-]*-g\)/r\1/;s/-/./g'
+}
+
+build() {
+  cd "${srcdir}/fgbio"
+  sbt assembly
+}
+
+check() {
+  cd "${srcdir}/fgbio"
+  sbt test
+}
+
+package() {
+  cd "${srcdir}/fgbio"
+  install -Dm644 target/scala-2.12/fgbio*.jar "${pkgdir}/usr/share/java/fgbio/fgbio.jar"
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/fgbio/LICENSE"
+  install -Dm644 README.md "${pkgdir}/usr/share/doc/fgbio/README.md"
+
+  cd "${srcdir}"
+  install -Dm755 "fgbio.sh" "${pkgdir}/usr/bin/fgbio"
+}
diff --git a/fgbio.sh b/fgbio.sh
new file mode 100644
index 000000000000..adc1a4511783
--- /dev/null
+++ b/fgbio.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+exec /usr/bin/java -jar '/usr/share/java/fgbio/fgbio.jar' "$@"