Package Details: ucsc-kent-genome-tools 379-1

Git Clone URL: https://aur.archlinux.org/ucsc-kent-genome-tools.git (read-only)
Package Base: ucsc-kent-genome-tools
Description: UCSC Kent bioinformatics utilities: kent source utilities
Upstream URL: http://hgdownload.soe.ucsc.edu/admin/exe/
Licenses: custom:UCSC
Submitter: greyltc
Maintainer: greyltc
Last Packager: greyltc
Votes: 4
Popularity: 0.000027
First Submitted: 2015-02-04 08:04
Last Updated: 2019-04-14 20:49

Latest Comments

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clintval commented on 2018-06-19 23:59

Hi all, we're stuck on v353 until upstream stops selective static linking. I've reached out to the community and if anyone is willing to make a patch for Arch that would be very appreciated.

Thanks!

clintval commented on 2018-06-19 15:24

@greyltc that's a great idea. I'll do it today, flag as out-of-date, and post a comment describing why we are struggling to rev up.

greyltc commented on 2018-06-19 13:49

@clintval, maybe you could roll this back to 366 until we ( you ;-) ) manage to get newer versions compiling?

clintval commented on 2018-06-08 18:44

I've reached out to the forum for help:

https://bbs.archlinux.org/viewtopic.php?pid=1790624#p1790624

clintval commented on 2018-05-01 18:20

This is going to require some work for successful compiling on Arch Linux. On all currently posted versions (up to v364) I get this error which is likely due to selective static linking:

/usr/lib/libm-2.26.a(s_rint.o): In function `__rint':
(.text+0x9): undefined reference to `_dl_x86_cpu_features'

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: