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AUR (en) - ucsc-kent-genome-tools

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Package Details: ucsc-kent-genome-tools 334-2

Git Clone URL: https://aur-dev.archlinux.org/ucsc-kent-genome-tools.git (read-only)
Package Base: ucsc-kent-genome-tools
Description: UCSC genome browser 'kent' bioinformatic utilities
Upstream URL: http://hgdownload.soe.ucsc.edu/admin/exe/
Licenses: Other
Submitter: greyltc
Maintainer: greyltc
Last Packager: greyltc
Votes: 3
Popularity: 0.031381
First Submitted: 2015-02-04 08:04
Last Updated: 2016-07-07 19:31

Latest Comments

greyltc commented on 2016-04-24 09:03

Should be fixed up and updated now. Apologies for the delay.

matrs commented on 2016-04-22 11:02

To solve the license problem, the license has to be between ().

matrs commented on 2016-03-22 13:46

install fails :
Proceed with installation? [Y/n] y
Edit ucsc-kent-genome-tools PKGBUILD with $EDITOR? [Y/n] n
Edit ucsc-kent-genome-tools.install with $EDITOR? [Y/n] n
==> ERROR: license should be an array
The build failed.

greyltc commented on 2016-01-08 15:19

updated to 326. sorry for the delay!

anpu commented on 2015-11-23 23:13

updated PKGBUILD (v324 released 2015-11-04, see http://hgdownload.cse.ucsc.edu/admin/exe/)

# Maintainer: Grey Christoforo <grey at christoforo dot net>

pkgname=ucsc-kent-genome-tools
pkgver=324
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=('21b51fca1e8034129ece70d680c21db6a493a8dd')

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:

greyltc commented on 2015-07-29 17:46

This package installs a large number of binaries. Some of the names of those collide with other binaries from random packages that you might not expect. This is a workaround.

flying-sheep commented on 2015-07-29 14:49

hi, a question: why do you put them into /usr/bin/kentUtils instead of somewhere in the PATH (e.g. /usr/bin)?