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* sci-biology/kat: various fixes for issue #867Fran├žois Bissey2018-05-071-69/+0
| | | | | | | | | | | | | | | | | | | | | | | many thanks to @kiwifb and @maplesond for on fixing the package and ebuild ax_check_zlib is in use. A hint for zlib location has to be provided otherwise system zlib will be used on prefix. make sure zlib is a dependency. develop branch has switched to proper library detection. fixing rpath. enabling python support (but broken right now). make sure a suitable python3 is setup at configure time bump to 2.4.2 fix typo in /DEPPEND/DEPEND/, cleanup comments Closes: https://github.com/gentoo/sci/issues/867 Closes: https://github.com/gentoo/sci/pull/868 Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/kat: properly install python filesMartin Mokrejs2018-04-231-16/+28
| | | | | | | | | | | | Thanks to kiwifb. Drop -8888, update -9999 and -2.4.1 to link against system-wide boost. No ebuilds left which would let the bundled boost slip in as a static library. See: https://github.com/TGAC/KAT/issues/94#issuecomment-383385701 Closes: https://github.com/gentoo/sci/issues/867 Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/kat: add missing DEPENDencyMartin Mokrejs2018-04-221-2/+3
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/kat: improve -8888 ebuildMartin Mokrejs2018-04-221-6/+6
| | | | | | | | | | | | | | | | | | | | | Try call setup.py on our own so that it could receive ${DESTDIR} contents. This still does not work. The ebuild drops bundled boost copy but retains bundled seqan headers and the modified copy of jellyfish. They won't interfere with with site-wide installed packages of those tools in Gentoo. The modified jellyfish is linked-in statically and binaries have 'kat_' prefix. The kat-2.4.1.ebuild and -9999.ebuild should later get same logic like appears in -8888.ebuild. Currently they stick to upstream's approach of using bundled boost too. All ebuilds suffer same problem: the python files do not get installed at all. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: ignore site-wide boost-build/site-config.jamMartin Mokrejs2018-04-221-3/+4
| | | | | | | Introduce -8888 ebuild which zaps bundled stuff altogether and uses system-wide boost and jellyfish2 files. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: execute the build_boost.sh and autogen.sh logicMartin Mokrejs2018-04-221-2/+13
| | | | | | | | Execute the commands from within ebuild to ease debugging of errors. See https://github.com/TGAC/KAT/issues/92 Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: version bumpMartin Mokrejs2018-04-211-0/+44
Lets require >=python-3.5 for best feature availability. The source code contain bundled sci-libs/boost and sci-biology/seqan. It also contain (unfortunately modified) sci-biology/jellyfish-2.2.0 https://github.com/TGAC/KAT/issues/92 Package-Manager: Portage-2.3.28, Repoman-2.3.9