38853 2004-01-20 15:32 0000 New ebuild phylip-3.6_beta 2004-07-19 17:46:13 0000 1 1 1 Unclassified Gentoo Linux Ebuilds unspecified x86 Linux RESOLVED FIXED http://evolution.genetics.washington.edu/phylip.html P2 enhancement --- 1 natunobilis@gentoobr.org sci@gentoo.org natunobilis@gentoobr.org 2004-01-20 15:32:09 0000 Phylip (PHYlogeny Inference Package) is a program package inferring phylogenies, written by Joseph Felsenstein at the University of Washington. Reproducible: Always Steps to Reproduce: 1. 2. 3. natunobilis@gentoobr.org 2004-01-20 15:35:19 0000 Created an attachment (id=24147) ebuild for v 3.6_beta of Phylip natunobilis@gentoobr.org 2004-01-20 15:36:24 0000 Created an attachment (id=24148) digest for v 3.6_beta of Phylip natunobilis@gentoobr.org 2004-01-21 14:28:15 0000 Apparently, I forgot to mention that although this is a beta version, the program's author (all-mighty Joe Felsenstein) strongly encourages its use. Even the alpha version was very reliable. ribosome@gentoo.org 2004-05-31 18:49:24 0000 I think many scientists would not want to use this beta version for producing results for publication. To make sure those who want can play with the beta while, at the same time, keeping the old version, we could make this package SLOTable. Here are two ebuilds for versions 3.5 and 3.6_beta1 that use the SLOT feature. Programs are installed in: /usr/phylip/3.x/bin. The relevant directory is added to PATH through the env file 24phylip. If both packages are installed, 24phylip adds the last installed version to PATH. Every user can override this by adding "export PATH=/usr/phylip/3.x/bin:$PATH" to his .bashrc. ribosome@gentoo.org 2004-05-31 18:55:13 0000 Created an attachment (id=32425) phylip-3.5-r1.ebuild - SLOTable ebuild ribosome@gentoo.org 2004-05-31 18:56:32 0000 Created an attachment (id=32426) phylip-3.6_beta1.ebuild - SLOTable ebuild ribosome@gentoo.org 2004-06-01 05:13:56 0000 Created an attachment (id=32441) phylip-3.6_beta1.ebuild - Corrected SLOTable ebuild There was a bug in my first 2.6 beta ebuild (I used PV instead of SLOT for determining DESTDIR, and PV includes the _beta1 part of the version). This corrected ebuild fixes that. ribosome@gentoo.org 2004-07-19 17:46:13 0000 Commited the new stable 3.6 version. 24147 2004-01-20 15:35 0000 ebuild for v 3.6_beta of Phylip phylip-3.6_beta.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA0IEdlbnRvbyBUZWNobm9sb2dpZXMsIEluYy4KIyBEaXN0cmli dXRlZCB1bmRlciB0aGUgdGVybXMgb2YgdGhlIEdOVSBHZW5lcmFsIFB1YmxpYyBMaWNlbnNlIHYy CgpERVNDUklQVElPTj0iUEhZTElQICh0aGUgUEhZTG9nZW55IEluZmVyZW5jZSBQYWNrYWdlKSBp cyBhIHBhY2thZ2Ugb2YgcHJvZ3JhbXMgZm9yIGluZmVycmluZyBwaHlsb2dlbmllcyAoZXZvbHV0 aW9uYXJ5IHRyZWVzKSIKCkhPTUVQQUdFPSJodHRwOi8vZXZvbHV0aW9uLmdlbmV0aWNzLndhc2hp bmd0b24uZWR1L3BoeWxpcC5odG1sIgpTUkNfVVJJPSJmdHA6Ly9ldm9sdXRpb24uZ2VuZXRpY3Mu d2FzaGluZ3Rvbi5lZHUvcHViL3BoeWxpcC9waHlsaXAzNi8ke1BOfS50YXIuZ3oiCkxJQ0VOU0U9 ImZyZWVkaXN0IgpTTE9UPSIwIgpLRVlXT1JEUz0ieDg2IgpJVVNFPSIiCkRFUEVORD0idmlydHVh bC9nbGliYyB2aXJ0dWFsL3gxMSIKCnNyY19jb21waWxlKCkgewoJY2QgJHtXT1JLRElSfS8ke1BO fS9zcmMKCUVYVFJBX0VNQUtFPSItZSAke0NGTEFHU30iCgllbWFrZSAtajEgaW5zdGFsbCB8fCBk aWUKfQoKc3JjX2luc3RhbGwoKQp7CgljZCAke1dPUktESVJ9LyR7UE59L2V4ZQoJZG9iaW4gY2xp cXVlIGNvbnNlbnNlIGNvbnRtbCBjb250cmFzdCBkbmFjb21wIGRuYWRpc3QgZG5haW52YXIKCWRv YmluIGRuYW1sIGRuYW1sayBkbmFtb3ZlIGRuYXBhcnMgZG5hcGVubnkgZG9sbG9wIGRvbG1vdmUK CWRvYmluIGRvbHBlbm55IGRyYXdncmFtIGRyYXd0cmVlIGZhY3RvciBmaXRjaCBnZW5kaXN0IGtp dHNjaAoJZG9iaW4gbWl4IG1vdmUgbmVpZ2hib3IgcGFycyBwZW5ueSBwcm9tbCBwcm9tbGsgcHJv dGRpc3QgcHJvdHBhcnMKCWRvYmluIHJlc3RkaXN0IHJlc3RtbCByZXRyZWUgc2VxYm9vdCB0cmVl ZGlzdAoJCgljZCAke1dPUktESVJ9LyR7UE59L2RvYwoJZG9kb2MgY2xpcXVlLmh0bWwgICAgZG5h bWxrLmh0bWwgICAgZml0Y2guaHRtbCAgICAgcHJvbWxrLmh0bWwKCWRvZG9jIGNvbnNlbnNlLmh0 bWwgIGRuYW1vdmUuaHRtbCAgIGdlbmRpc3QuaHRtbCAgIHByb3RkaXN0Lmh0bWwKCWRvZG9jIGNv bnRjaGFyLmh0bWwgIGRuYXBhcnMuaHRtbCAgIGtpdHNjaC5odG1sICAgIHByb3RwYXJzLmh0bWwK CWRvZG9jIGNvbnRtbC5odG1sICAgIGRuYXBlbm55Lmh0bWwgIG1haW4uaHRtbCAgICAgIHJlc3Rk aXN0Lmh0bWwKCWRvZG9jIGNvbnRyYXN0Lmh0bWwgIGRvbGxvcC5odG1sICAgIG1peC5odG1sICAg ICAgIHJlc3RtbC5odG1sCglkb2RvYyBkaXNjcmV0ZS5odG1sICBkb2xtb3ZlLmh0bWwgICBtb3Zl Lmh0bWwgICAgICByZXRyZWUuaHRtbAoJZG9kb2MgZGlzdGFuY2UuaHRtbCAgZG9scGVubnkuaHRt bCAgbmVpZ2hib3IuaHRtbCAgc2VxYm9vdC5odG1sCglkb2RvYyBkbmFjb21wLmh0bWwgICBkcmF3 Z3JhbS5odG1sICBwYXJzLmh0bWwgICAgICBzZXF1ZW5jZS5odG1sCglkb2RvYyBkbmFkaXN0Lmh0 bWwgICBkcmF3Lmh0bWwgICAgICBwZW5ueS5odG1sICAgICB0cmVlZGlzdC5odG1sCglkb2RvYyBk bmFpbnZhci5odG1sICBkcmF3dHJlZS5odG1sICBwaHlsaXAuZ2lmCglkb2RvYyBkbmFtbC5odG1s ICAgICBmYWN0b3IuaHRtbCAgICBwcm9tbC5odG1sCn0KCg== 24148 2004-01-20 15:36 0000 digest for v 3.6_beta of Phylip digest-phylip-3.6_beta text/plain TUQ1IGFlNmRkMzNhYzUxNjgyNTI3ZjViZjFmZGNlZjZkMDUwIHBoeWxpcC50YXIuZ3ogODMxOTA1 Cg== 32425 2004-05-31 18:55 0000 phylip-3.5-r1.ebuild - 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