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authorGrey Christoforo2015-06-20 19:55:05 +0200
committerGrey Christoforo2015-06-20 19:55:05 +0200
commitfc48d1648e046d29ed31f6e3fa89e3a74efc0d00 (patch)
tree64abf9b8732b062f1679181e10bf4ec88b3e065d
downloadaur-fc48d1648e046d29ed31f6e3fa89e3a74efc0d00.tar.gz
Initial import
-rw-r--r--.SRCINFO17
-rw-r--r--PKGBUILD41
-rw-r--r--ucsc-kent-genome-tools.install13
3 files changed, 71 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 00000000000..2369342a523
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,17 @@
+pkgbase = ucsc-kent-genome-tools
+ pkgdesc = UCSC genome browser 'kent' bioinformatic utilities
+ pkgver = 316
+ pkgrel = 1
+ url = http://hgdownload.soe.ucsc.edu/admin/exe/
+ install = ucsc-kent-genome-tools.install
+ arch = i686
+ arch = x86_64
+ license = other
+ depends = mariadb-clients
+ depends = libpng
+ depends = openssl
+ source = http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v316.src.tgz
+ sha1sums = b9eddc7e7bce7d3f6a2b09d06175b9ebee776764
+
+pkgname = ucsc-kent-genome-tools
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 00000000000..ba79e289c79
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,41 @@
+# Maintainer: Grey Christoforo <grey at christoforo dot net>
+
+pkgname=ucsc-kent-genome-tools
+pkgver=316
+pkgrel=1
+pkgdesc="UCSC genome browser 'kent' bioinformatic utilities"
+arch=('i686' 'x86_64')
+url="http://hgdownload.soe.ucsc.edu/admin/exe/"
+license=other
+install=$pkgname.install
+depends=('mariadb-clients' 'libpng' 'openssl')
+source=(http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${pkgver}.src.tgz)
+sha1sums=('b9eddc7e7bce7d3f6a2b09d06175b9ebee776764')
+
+build() {
+ cd "${srcdir}/userApps/"
+ make
+}
+
+package() {
+ cd "${srcdir}/userApps/"
+ mkdir -p "${pkgdir}/usr/bin/"
+ mv bin/ "${pkgdir}/usr/bin/kentUtils/"
+
+ mkdir -p "$pkgdir/etc/profile.d"
+ echo "export PATH=/usr/bin/kentUtils:"'$PATH' > "$pkgdir/etc/profile.d/kentUtils.sh"
+
+ mkdir -p "${pkgdir}/opt/kentUtils/"
+cat > "${pkgdir}/opt/kentUtils/.hg.conf" <<EOF
+db.host=genome-mysql.cse.ucsc.edu
+db.user=genomep
+db.password=password
+central.db=hgcentral
+EOF
+
+ install -D -m644 licenseUcscGenomeBrowser.txt "${pkgdir}/usr/share/licenses/kentUtils/licenseUcscGenomeBrowser.txt"
+ install -D -m644 GenomeBrowserLicense.pdf "${pkgdir}/usr/share/licenses/kentUtils/GenomeBrowserLicense.pdf"
+ install -D -m644 licenseBlat.txt "${pkgdir}/usr/share/licenses/kentUtils/licenseBlat.txt"
+}
+
+# vim:set ts=2 sw=2 et:
diff --git a/ucsc-kent-genome-tools.install b/ucsc-kent-genome-tools.install
new file mode 100644
index 00000000000..9b9a9213a8d
--- /dev/null
+++ b/ucsc-kent-genome-tools.install
@@ -0,0 +1,13 @@
+## arg 1: the new package version
+post_install() {
+ echo
+ echo "To enable access to the UCSC SQL database, run the following for each user:"
+ echo "cp /opt/kentUtils/.hg.conf ~/."
+ echo "chmod 600 ~/.hg.conf"
+ echo
+ echo "To use the tools, log out and log back in to use the tools, or run"
+ echo "source /etc/profile"
+ echo "To enable them immediately"
+ echo
+}
+