diff options
author | Lionel Miller | 2018-07-18 15:09:11 +0300 |
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committer | Lionel Miller | 2018-07-18 15:15:56 +0300 |
commit | a6381030d5122ee67f70b04d9286d36ff9d23c3e (patch) | |
tree | a244382d7f15b8942510268ced85feba11c5ec02 | |
download | aur-a6381030d5122ee67f70b04d9286d36ff9d23c3e.tar.gz |
Initial version
-rw-r--r-- | .SRCINFO | 20 | ||||
-rw-r--r-- | PKGBUILD | 46 | ||||
-rw-r--r-- | gatk.sh | 39 |
3 files changed, 105 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..80176876df9e --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,20 @@ +pkgbase = gatk-bin + pkgdesc = Variant discovery in high-throughput bioinformatics sequencing data + pkgver = 4.0.6.0 + pkgrel = 1 + url = https://software.broadinstitute.org/gatk-bin + arch = any + license = BSD + depends = java-environment=8 + depends = python + optdepends = r: plot generation for some tools + conflicts = gatk + source = gatk-bin-4.0.6.0.zip::https://github.com/broadinstitute/gatk/releases/download/4.0.6.0/gatk-4.0.6.0.zip + source = gatk.sh + source = gatk-bin-license.txt::https://raw.githubusercontent.com/broadinstitute/gatk/d6a7fcd895677424b491df8c4ee6227e34b52251/LICENSE.TXT + sha512sums = 6d2247ed5f06e61b561347c8d09cc789b38ad0ea7ab254036b0d9638a9c839ba128427cfed146c525f981fae407eb0448b2e10d0a68e679c297872cb19d25a0f + sha512sums = a9984153bc489bf5814adc8f8bffd92782e7dd031f2b9a0798d2dc005438445f5eefed6ce3b64b776197c49fb8579e4c968e7cdc4398c5df0145e5105cc20271 + sha512sums = 9753eef4b1f3aa96b790eaeacbe92ecb9d8fee6de9b918244a519a53b5285d57d2128e62f6a86c5d931d217a72f08e806ff81e95ad8d271c1df737384c81e30e + +pkgname = gatk-bin + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..b6077bf4d9b7 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Lionel Miller <delonorm@gmail.com> + +pkgname=gatk-bin +pkgver=4.0.6.0 +pkgrel=1 +pkgdesc="Variant discovery in high-throughput bioinformatics sequencing data" +arch=('any') +url=https://software.broadinstitute.org/"${pkgname}" +license=('BSD') +depends=('java-environment=8' 'python') +optdepends=('r: plot generation for some tools') +conflicts=('gatk') +source=( + "${pkgname}-${pkgver}.zip::https://github.com/broadinstitute/gatk/releases/download/${pkgver}/gatk-${pkgver}.zip" + gatk.sh + "${pkgname}-license.txt::https://raw.githubusercontent.com/broadinstitute/gatk/d6a7fcd895677424b491df8c4ee6227e34b52251/LICENSE.TXT" +) +sha512sums=( + '6d2247ed5f06e61b561347c8d09cc789b38ad0ea7ab254036b0d9638a9c839ba128427cfed146c525f981fae407eb0448b2e10d0a68e679c297872cb19d25a0f' + 'a9984153bc489bf5814adc8f8bffd92782e7dd031f2b9a0798d2dc005438445f5eefed6ce3b64b776197c49fb8579e4c968e7cdc4398c5df0145e5105cc20271' + '9753eef4b1f3aa96b790eaeacbe92ecb9d8fee6de9b918244a519a53b5285d57d2128e62f6a86c5d931d217a72f08e806ff81e95ad8d271c1df737384c81e30e' +) + +package() { + # I am using the launcher script from the source-based gatk package + # instead of the official Python launcher because Python launcher is + # far more complex than this script, and I have not investigated in + # detail what it does. + install -Dm755 gatk.sh "${pkgdir}"/usr/bin/gatk + + # Downloading the license separately because it is not included + # in the distribution, and namcap complains if it is not installed. + install -Dm644 "${pkgname}-license.txt" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE.TXT" + + # Resing much of the installation procedure from the source-based package. + cd "${srcdir}/gatk-${pkgver}" + install -Dm644 README.md "${pkgdir}"/usr/share/doc/"${pkgname}"/README.md + install -Dm644 "gatk-package-${pkgver}-local.jar" "${pkgdir}/usr/share/java/${pkgname}/GenomeAnalysisTK.jar" + install -Dm644 "gatk-completion.sh" "${pkgdir}/usr/share/bash-completion/completions/gatk" + + # Things that are missing: + # 1. spark executable (maybe it should go in a separate package) + # 2. gatkdoc + # 3. scripts + # 4. Python launcher (not sure whether it is superior to the current one) +} diff --git a/gatk.sh b/gatk.sh new file mode 100644 index 000000000000..d105ecad017e --- /dev/null +++ b/gatk.sh @@ -0,0 +1,39 @@ +#!/usr/bin/env bash + +set -eou pipefail +export LC_ALL=en_US.UTF-8 + +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" + +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval java $jvm_mem_opts $jvm_prop_opts -cp '/usr/share/java/gatk-bin/GenomeAnalysisTK.jar' $pass_args +else + eval java $jvm_mem_opts $jvm_prop_opts -jar '/usr/share/java/gatk-bin/GenomeAnalysisTK.jar' $pass_args +fi +exit |