First commit with PKGBUILD, .SRCINFO, rtg.cfg, and rtg.sh for bash completions

4 files changed, 146 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..b2364c22ee2b
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,19 @@
+pkgbase = rtg-tools
+	pkgdesc = Utilities for accurate VCF comparison and manipulation
+	pkgver = 3.8.4
+	pkgrel = 1
+	url = https://github.com/RealTimeGenomics/rtg-tools
+	arch = i686
+	arch = x86_64
+	license = Simplified BSD
+	makedepends = apache-ant>1.9
+	depends = java-runtime>=1.8
+	source = https://github.com/RealTimeGenomics/rtg-tools/archive/3.8.4.tar.gz
+	source = rtg.cfg
+	source = rtg.sh
+	md5sums = c5b558cbe845fcb315e943162b7da38e
+	md5sums = 1e5e1f5df474ab87b5a28a9d694e4e17
+	md5sums = 64a6dc8d7c7ed9c3e0ba3d8c42f8194d
+
+pkgname = rtg-tools
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..6b21c6ee407a
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,58 @@
+# Maintainer: Clint Valentine <valentine.clint@gmail.com>
+
+pkgname=rtg-tools
+pkgver=3.8.4
+pkgrel=1
+pkgdesc="Utilities for accurate VCF comparison and manipulation"
+arch=('i686' 'x86_64')
+url="https://github.com/RealTimeGenomics/rtg-tools"
+license=('Simplified BSD')
+depends=('java-runtime>=1.8')
+makedepends=('apache-ant>1.9')
+source=(
+  "https://github.com/RealTimeGenomics/${pkgname}/archive/${pkgver}.tar.gz"
+  "rtg.cfg"
+  "rtg.sh")
+md5sums=(
+  'c5b558cbe845fcb315e943162b7da38e'
+  '1e5e1f5df474ab87b5a28a9d694e4e17'
+  '64a6dc8d7c7ed9c3e0ba3d8c42f8194d')
+
+build() {
+  cd "${srcdir}/${pkgname}-${pkgver}"
+  ant zip-nojre
+  unzip -qn dist/rtg-tools-3.8.4-*-nojre.zip
+}
+
+check() {
+  cd "${srcdir}/${pkgname}-${pkgver}"
+  ant runalltests
+}
+
+package() {
+  cd "${srcdir}"
+  # Add environment variable to specify custom location of RTG.jar
+  install -Dm655 rtg.cfg "${pkgdir}/etc/rtg.cfg"
+  echo "RTG_JAR=/usr/share/java/${pkgname}/RTG.jar" >> "${pkgdir}/etc/rtg.cfg"
+
+  # Install primary JAR file
+  cd "${srcdir}/${pkgname}-${pkgver}/${pkgname}-${pkgver}-"*
+  install -Dm655 RTG.jar "${pkgdir}/usr/share/java/${pkgname}/RTG.jar"
+
+  # Remove the need for a local configuration file, respect only system config
+  install -Dm755 rtg "${pkgdir}/usr/bin/rtg"
+  sed -i "s#\$THIS_DIR/rtg.cfg#${pkgdir}/etc/rtg.cfg#g" "${pkgdir}/usr/bin/rtg"
+
+  # Install demo script, data, and bash completions scrips
+  cp -r scripts "${pkgdir}/usr/share/${pkgname}"
+
+  # Install completion hook in profile.d to be sourced with each shell
+  install -Dm755 "scripts/rtg-bash-completion" "${pkgdir}/etc/profile.d/rtg-bash-completer.sh"
+
+  # Licenses and documentation
+  install -Dm655 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE.txt"
+  install -Dm655 README.txt "${pkgdir}/usr/share/doc/${pkgname}/README.txt"
+  install -Dm655 ReleaseNotes.txt "${pkgdir}/usr/share/doc/${pkgname}/ReleaseNotes.txt"
+  install -Dm655 RTGOperationsManual.pdf "${pkgdir}/usr/share/doc/${pkgname}/RTGOperationsManual.pdf"
+  cp -r RTGOperationsManual "${pkgdir}/usr/share/doc/${pkgname}/RTGOperationsManual"
+}
diff --git a/rtg.cfg b/rtg.cfg
new file mode 100644
index 000000000000..ffc448b78fe0
--- /dev/null
+++ b/rtg.cfg
@@ -0,0 +1,68 @@
+# Configuration file for RTG.
+
+# This file is automatically created upon first run, and may be edited
+# to allow some customization of default behaviour.  In a
+# multi-machine environment, this file can be used to achieve
+# machine-specific configuration either by placing in /etc/rtg.cfg on
+# each machine or in the rtg installation directory values with the
+# name rtg.$(hostname -s).cfg, e.g. rtg.bioinformatics.cfg
+
+
+# The path to the java executable (need not be full path if in $PATH).
+# If unset, RTG will use the bundled JRE if present, otherwise
+# will expect java to be on $PATH
+# RTG_JAVA="java"
+
+# Amount of memory to allocate to RTG.  Use G suffix for gigabytes.
+# If unset, allow RTG to use up to 90% of available RAM (see RTG_MEM_PCT)
+# RTG_MEM="4G"
+# Note that memory allocation can also be overridden on a per-command basis, e.g:
+# $ rtg RTG_MEM=24G population ...
+
+# If RTG_MEM is unset, use this percentage of total RAM.
+# The default is 90 percent.
+# RTG_MEM_PCT=90
+
+
+# Attempt to send crash logs to Real Time Genomics, true to enable, false to disable
+RTG_TALKBACK=false
+
+# Enable simple usage logging, true to enable. Default is no logging.
+RTG_USAGE=
+
+# Server URL when usage logging to a server. Default is to use RTG hosted server.
+# RTG_USAGE_HOST=
+
+# If performing single-user file-based usage logging, this specifies the directory to log to.
+# RTG_USAGE_DIR=
+
+# List of optional fields to add to usage logging (when enabled).
+# If unset do not add any of these fields. (commandline may contain information
+# considered sensitive)
+# RTG_USAGE_OPTIONAL=username,hostname,commandline
+RTG_USAGE_OPTIONAL=username,hostname
+
+
+# Allows specification of the HTTP proxy to use for
+# talkback/usage, specified in host:port form.
+# If unset, assume no http proxy is required.
+# RTG_PROXY=my.proxy.host:3128
+
+
+# Directory in which to look for pipeline reference datasets.
+# If unset, uses the references subdirectory of this installation.
+# RTG_REFERENCES_DIR=
+
+# Directory in which to look for AVR models.
+# If unset, uses the models subdirectory of this installation.
+# RTG_MODELS_DIR=
+
+# Allows passing additional arguments passed to the JVM. e.g:
+# RTG_JAVA_OPTS="-Djava.io.tmpdir=XXYY -XX:+UseLargePages"
+
+
+# Set the number of threads to use when not otherwise specified via command line flags.
+# The default behavior is to allocate one thread per machine core.
+# RTG_DEFAULT_THREADS=1
+
+
diff --git a/rtg.sh b/rtg.sh
new file mode 100755
index 000000000000..8ce677e7891f
--- /dev/null
+++ b/rtg.sh
@@ -0,0 +1 @@
+source /etc/share/rtg-tools/rtg-bash-completion