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author | clintval | 2018-01-21 14:36:18 -0800 |
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committer | clintval | 2018-01-21 14:36:18 -0800 |
commit | d4124ef5e04b906df01eab25456bfc2b9144ba8a (patch) | |
tree | fc26f0ea57e5844dfaf7f1bfc7589026a6c778b1 | |
parent | fdcfa7039fd9a5b6d75c5d34540256c03804daf1 (diff) | |
download | aur-d4124ef5e04b906df01eab25456bfc2b9144ba8a.tar.gz |
ucsc-kent-genome-tools to v348
-rw-r--r-- | PKGBUILD | 65 | ||||
-rw-r--r-- | ucsc-kent-genome-tools.install | 2 | ||||
-rw-r--r-- | ucsc-kent-genome-tools.sh | 1 |
3 files changed, 32 insertions, 36 deletions
@@ -1,51 +1,48 @@ -# Maintainer: Grey Christoforo <first name [at] last name [dot] net> +# Maintainer: Clint Valentine <valentine.clint@gmail.com> +# Contributer: Grey Christoforo <first name [at] last name [dot] net> pkgname=ucsc-kent-genome-tools -pkgver=347 +pkgver=348 pkgrel=1 -pkgdesc="UCSC genome browser 'kent' bioinformatic utilities" -arch=('i686' 'x86_64') +pkgdesc="UCSC Kent bioinformatics utilities: kent source utilities" +arch=('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=('25b6351f795f11e95e061b00dfd1b027dc4dd776') +license=('custom:UCSC') +install="${pkgname}".install +depends=('libpng' 'mariadb-clients' 'uuid' 'openssl') +source=( + .hg.conf + "${pkgname}".sh + "${pkgname}"-"${pkgver}".src.tgz::http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v"${pkgver}".src.tgz +) +sha256sums=( + '359db5b022847d3d674f21821fa08a363d2183379d59a2b63129fcf90954d674' + '926eb0ff0bdce64d6a3439647d8b7c639b26a7211d9eee11bdaab9bd473c0959' + '8ef45648fd4d022d33fd57f1dd2702a56074364eea3c3334d77f501128f390a5' +) prepare() { - cd "${srcdir}/userApps/" + cd "${srcdir}"/userApps make clean } build() { - cd "${srcdir}/userApps/" - # don't know why I need the next three lines - make libs - cp kent/src/lib/x86_64/* kent/src/lib/local/. - cp kent/src/lib/local/* kent/src/lib/x86_64/. + cd "${srcdir}"/userApps make all } package() { - cd "${srcdir}/userApps/" - mkdir -p "${pkgdir}/opt/${pkgname}/" - cp -a * "${pkgdir}/opt/${pkgname}/." - rm -rf "${pkgdir}/opt/${pkgname}/kent" + install -Dm644 .hg.conf "${pkgdir}"/opt/"${pkgname}"/.hg.conf + install -Dm755 "${pkgname}".sh "${pkgdir}"/etc/profile.d/"${pkgname}".sh - mkdir -p "$pkgdir/etc/profile.d" - echo "export PATH=/opt/${pkgname}/bin:"'$PATH' > "$pkgdir/etc/profile.d/${pkgname}.sh" - chmod +x "$pkgdir/etc/profile.d/${pkgname}.sh" + for script in "${srcdir}"/userApps/bin/*; do + install -Dm755 "${script}" "${pkgdir}"/opt/"${pkgname}"/$(basename "${script}") + done - cat > "${pkgdir}/opt/${pkgname}/.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 "${pkgdir}/usr/share/licenses/${pkgname}/licenseUcscGenomeBrowser.txt" - install -D -m644 GenomeBrowserLicense.pdf "${pkgdir}/usr/share/licenses/${pkgname}/GenomeBrowserLicense.pdf" - install -D -m644 licenseBlat.txt "${pkgdir}/usr/share/licenses/${pkgname}/licenseBlat.txt" -} + install -Dm644 "${srcdir}"/userApps/README "${pkgdir}"/usr/share/doc/"${pkgname}"/README + install -Dm644 "${srcdir}"/userApps/kentUtils.Documentation.txt "${pkgdir}"/usr/share/doc/"${pkgname}"/kentUtils.Documentation.txt -# vim:set ts=2 sw=2 et: + install -Dm644 "${srcdir}"/userApps/licenseUcscGenomeBrowser.txt "${pkgdir}"/usr/share/licenses/"${pkgname}"/licenseUcscGenomeBrowser.txt + install -Dm644 "${srcdir}"/userApps/GenomeBrowserLicense.pdf "${pkgdir}"/usr/share/licenses/"${pkgname}"/GenomeBrowserLicense.pdf + install -Dm644 "${srcdir}"/userApps/licenseBlat.txt "${pkgdir}"/usr/share/licenses/"${pkgname}"/licenseBlat.txt +} diff --git a/ucsc-kent-genome-tools.install b/ucsc-kent-genome-tools.install index 9b9a9213a8d3..e977b86f556c 100644 --- a/ucsc-kent-genome-tools.install +++ b/ucsc-kent-genome-tools.install @@ -1,4 +1,3 @@ -## arg 1: the new package version post_install() { echo echo "To enable access to the UCSC SQL database, run the following for each user:" @@ -10,4 +9,3 @@ post_install() { echo "To enable them immediately" echo } - diff --git a/ucsc-kent-genome-tools.sh b/ucsc-kent-genome-tools.sh new file mode 100644 index 000000000000..1a5c2d8524ce --- /dev/null +++ b/ucsc-kent-genome-tools.sh @@ -0,0 +1 @@ +export PATH=/opt/ucsc-kent-genome-tools/bin:$PATH |