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Package Details: ucsc-kent-genome-tools 405-1
Git Clone URL: | https://aur.archlinux.org/ucsc-kent-genome-tools.git (read-only, click to copy) |
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Package Base: | ucsc-kent-genome-tools |
Description: | UCSC Kent bioinformatics utilities: kent source utilities |
Upstream URL: | http://hgdownload.soe.ucsc.edu/admin/exe/ |
Licenses: | |
Submitter: | greyltc |
Maintainer: | greyltc |
Last Packager: | greyltc |
Votes: | 4 |
Popularity: | 0.000000 |
First Submitted: | 2015-02-04 08:04 |
Last Updated: | 2020-11-01 19:30 |
Dependencies (4)
- libpng (libpng-git, libpng-apng, libpng-minimal-git)
- mariadb-clients (mysql-clients55, mariadb-clients-git, mariadb103-clients, mysql-clients56, mysql-clients57, mysql-clients, percona-server-clients)
- openssl (libressl-git, openssl-purify, openssl-zlib, openssl-git, openssl-weak-ciphers, openssl-hardened)
- uuid
Required by (5)
- homer (optional)
- python-pybedtools (optional)
- python-pybedtools-git (optional)
- python2-pybedtools (optional)
- python2-pybedtools-git (optional)
Latest Comments
1 2 Next › Last »
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 I'll do it today, flag as out-of-date, and post a comment describing why we are struggling to rev up.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:
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: