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)
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: 0.000000
First Submitted: 2015-02-04 08:04 (UTC)
Last Updated: 2020-11-01 19:30 (UTC)

Latest Comments

AndreasSchild commented on 2022-01-26 12:01 (UTC)

Hi Chrisoforo, the Downloadlink has changed. Could You please make the following changes to PKGBUILD. Thanks a lot in advance, Andreas

pkgver=425 source=( .hg.conf "${pkgname}".sh "${pkgname}"-"${pkgver}".src.tgz::http://hgdownload.soe.ucsc.edu/admin/exe/userApps.src.tgz )

sha256sums=('359db5b022847d3d674f21821fa08a363d2183379d59a2b63129fcf90954d674' 20 '5ccec9d5e4de9be22746fab1591127b61176c8c4d586c0dd1df13ee5e52a5367' 21 'd70252a70cce7cc870666506c66604b307de8dc0634130fdbd4ac0547e0815ce')

balwierz commented on 2021-10-18 11:39 (UTC) (edited on 2021-10-18 11:48 (UTC) by balwierz)

out of date and broken. The need to add "userApps.archive" to the source URL.

moreover, after tweaking PKGBUILD linking fails: /usr/bin/ld: ../../lib/local/jkweb.a(portimpl.o):/tmp/yaourt-tmp-piotr/aur-ucsc-kent-genome-tools/src/userApps/kent/src/lib/../inc/htmshell.h:163: multiple definition of `htmlRecover'; ../../lib/local/jkweb.a(cheapcgi.o):/tmp/yaourt-tmp-piotr/aur-ucsc-kent-genome-tools/src/userApps/kent/src/lib/../inc/htmshell.h:163: first defined here

clintval commented on 2018-06-19 23:59 (UTC)

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 (UTC)

@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 I'll do it today, flag as out-of-date, and post a comment describing why we are struggling to rev up.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 (UTC)

@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 (UTC)

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 (UTC)

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 (UTC)

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

matrs commented on 2016-04-22 11:02 (UTC)

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

matrs commented on 2016-03-22 13:46 (UTC)

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 (UTC)

updated to 326. sorry for the delay!

anpu commented on 2015-11-23 23:13 (UTC)

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 (UTC)

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 (UTC)

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