commit 7e11364f3429ea8e4662a5c245c23e53a498326c
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 29 14:07:02 2019 +0100

sci-biology/augustus: fix typo in a comment line

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit dad62d03f97e438406e58011f360195638297858
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 29 14:05:38 2019 +0100

sci-biology/augustus: adjust to current LICENSE, use $

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit f291cafdf1bac38dea4e9781f08ee7cc171a6dc4
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 29 14:00:21 2019 +0100

sci-biology/augustus: version bump, fix awful Makefile's

Do not require static libraries. Only bamtools are really needed.
htslib is not needed. For bam2wig samtools-0.2 series is needed.

I decided to blindly install some of the binaries created but not
copied into `./bin/`.

`src/Makefile` will gladly define mysql and sqlite together, probably
a non-sense. We force mysql as we check for it first. Not sure if
sqlite should be preferred.

I documented in the augustus-3.3.2.ebuild other "forgotten" files,
like gbrowse.conf and a template for gff2ps.

I dropped `-O3` but left in `-ggdb` in the `CXXFLAGS`.

https://github.com/Gaius-Augustus/Augustus/issues/14
https://github.com/Gaius-Augustus/Augustus/issues/50
https://github.com/Gaius-Augustus/Augustus/issues/51
https://github.com/Gaius-Augustus/Augustus/issues/52
https://github.com/Gaius-Augustus/Augustus/issues/53

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit e38217259584ffe970ca141a51274da2265efbe6
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Mar 31 02:38:30 2018 +0200

sci-biology/augustus: update file checksum

Seems upstream re-released the binary tarball with sources

$ gzip -dc /usr/portage/distfiles/augustus-3.3.tar.gz | tar tvf - | grep 2018
drwxrwxr-x mario/mario 0 2018-01-26 14:09 augustus/auxprogs/homGeneMapping/src/
drwx------ mario/mario 0 2018-01-26 14:07 augustus/auxprogs/joingenes/
drwx------ mario/mario 0 2018-01-26 14:07 augustus/auxprogs/bam2hints/
drwx------ mario/mario 0 2018-01-26 14:09 augustus/auxprogs/filterBam/src/
drwxrwxr-x mario/mario 0 2018-01-26 14:09 augustus/auxprogs/filterBam/bin/
drwxrwxr-x mario/mario 0 2018-01-26 14:07 augustus/auxprogs/compileSpliceCands/
drwx------ mario/mario 0 2018-01-26 14:08 augustus/auxprogs/bam2wig/
drwx------ mario/mario 0 2018-01-26 14:08 augustus/bin/

Package-Manager: Portage-2.3.24, Repoman-2.3.6

commit edf1cd8c7acd0369e94308ab5cdbcfea6c81e50b
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 23 01:47:46 2018 +0100

sci-biology/augustus: respect EPREFIX and new DEPENDency

The dependency is brought in through the comparative gene prediction
code.

Package-Manager: Portage-2.3.24, Repoman-2.3.6

commit cf04df0e7dad1b7779e01e24071a3c3600e2cebf
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 23 01:22:22 2018 +0100

sci-biology/augustus: respect EPREFIX and enable comparative gene prediction

Package-Manager: Portage-2.3.24, Repoman-2.3.6

commit f1edfa4859b565410b78bbde88c93185b68dfe43
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jan 8 14:53:47 2018 +0100

sci-biology/augustus: version bump

Package-Manager: Portage-2.3.19, Repoman-2.3.6

commit 3072d10e6c4f21185d53e4728d0fa0fad58537e7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Dec 10 22:20:38 2017 +0000

Update Manifests to new hashes

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit bce61aa3e4fe85fe411df858eb30ebe72a3a8f88
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Nov 18 20:39:44 2017 +0000

Consistently ident with tabs

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit f69e73182fc7cdc6c600a72fceb88ae1626db25d
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Feb 25 16:50:59 2017 +0000

Drop leftover from CVS in HEADER

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit f27843ff427867921374d9b23f9f074be211e191
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 1 19:44:01 2016 +0100

sci-biology/augustus: zap -O3 CFLAG from src/Makefile

Package-Manager: portage-2.3.2

commit 057a98c5e6346d6696fcc7b0ec8fefc9e826245f
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:53:09 2016 +0100

metadata.xml: Set type

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit b9d823e1ea1018d1356a0c18a083eab4d5ea6d8d
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:50:12 2016 +0100

metadata.xml: convert hard -> proj

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 2ef24e800910be3786e23a31a0217ba0f38659f8
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Jan 7 15:10:39 2016 +0100

Drop ChangeLogs in favour of commit messages

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit e71d7ff2098227500cd475827ab40d0a79fccca1
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Sep 23 14:47:23 2015 +0200

sci-biology/augustus: Use default functions

Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 6271f0c55cbb6af7fe88ae1ec9d7dbdedd562565
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Aug 17 08:53:12 2015 +0200

Convert all $Header$ to $Id$ tags as it has be done in gentoo.git

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit a891336052fb27fd9f3f82e33c30f0984f50ea54
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:25:27 2015 +0200

Revert "Gentoo does https by default now"

This reverts commit 98718494343af4990facdefb0033471686e975a6.

commit 98718494343af4990facdefb0033471686e975a6
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:14:25 2015 +0200

Gentoo does https by default now

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 474dc964e9ffb57968a6fc0393ca8dda8524ff53
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon May 25 21:06:52 2015 +0200

sci-biology/augustus: version bump

Package-Manager: portage-2.2.18

commit 73279dca5c2ff3b859c936ae0fac7c5b2903addf
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Apr 16 08:26:59 2015 +0200

sci-biology/augustus: Switch RDEPEND - DEPEND

Package-Manager: portage-2.2.18

commit a94334503b1305007f699b8c586467390140cbf2
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Apr 15 11:37:16 2015 +0200

Drop CVS keywords

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 2c793fdd99a16242897e0ae5f838156723b87ca6
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Apr 8 11:44:32 2015 +0200

sci-biology/augustus: Drop suspect DEPEND

Package-Manager: portage-2.2.18

commit d80145ef93597dea34ba14fb06ee4975740c6c84
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Mar 31 00:44:17 2015 +0200

sci-biology/augustus: version bump, new license (temporarily), new dependencies since 3.0 series

Package-Manager: portage-2.2.18