biology/ugene: fix build on aarch64

The bundled copy of htslib is missing required assembly source files,
causing build failure due to undefined symbols an aarch64.
Unbundle htslib and use our working port biology/htslib instead.

Approved by:	makc (maintainer)
MFH:		2026Q2
PR:		293379

biology/ugene: Update to 53.1

Release Notes: https://ugene.net/changelist.html

Port changes:
- Fix build on non-x86, mark IGNORE for aarch64.
- Switch to cmake, qmake is not supported anymore.
- Drop unused sqlite, renew Qt components.
- Convert to PORTDATA, use shebangfix.

Special thanks to fuz@ for testing and fixing non-x86 build!

PR:		293379

biology/ugene: adopt

biology/ugene: return to pool

PR:		293379

MAN?PREFIX: eleminate its usage  and move man to share/man

Mk/Uses: always use colon for build/run suffix

Most USES use a colon for build/run(/test) suffixes. Change kde.mk,
qt.mk and pyqt.mk to do the same, and update all ports using that.

Document in CHANGES.

PR:			266034
Exp-run by:		antoine
Approved by:		tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D36349

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

biology/ugene: Correct BROKEN message

Approved by:	portmgr (blanket)

biology/ugene: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
Approved by:	portmgr (blanket)

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>

biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).

biology/ugene: update Unipro UGENE to version 40.0.

biology/ugene: update Unipro UGENE to version 39.0.

graphics/mesa-libs: Bump reverse deps for libglvnd

Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.

PR:		246767
Reviewed by:	manu, bapt
Approved by:	x11
Differential Revision:	https://reviews.freebsd.org/D30824

- Update Unipro UGENE to version 38.1 and thus unbreak
- CONFIG defaults to 64-bit mode now, adjust the check

biology/ugene: mark BROKEN (does not fetch)

Approved by:	portmgr blanket

Remove # $FreeBSD$ from Makefiles.

- Update Unipro UGENE to version 38.0
- Garbage-collect no longer needed patches
- Make COMMENT shorter and closer to upstream
- Stop building bundled SQLite, use ours!

Mark BROKEN on riscv64 the same as on aarch64.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com build testing

- Update Unipro UGENE port to version 37.0
- Drop no longer used WebEngine dependencies
- Force SSE2 on i386 (required for the build)
- Chase HTTP 301 redirection in the WWW line

biology/ugene: prepare for Qt5-5.15

- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead

Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months

Deprecate ports broken for more than 6 months

Mark a few ports BROKEN, unfetchable

Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.

Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call

Update Qt5 to 5.12.0

http://blog.qt.io/blog/2018/12/06/qt-5-12-lts-released/

- This breaks support for libressl again. Patches are welcome.

PR:		233705
Exp-run by:	antoine

Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)

Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk

From now on, ports that depend on Qt4 will have to set
	USES=		qt:4
	USE_QT=		foo bar
ports depending on Qt5 will use
	USES=		qt:5
	USE_QT=		foo bar

PR:		229225
Exp-run by:	antoine
Reviewed by:	mat
Approved by:	portmgr (antoine)
Differential Revision:	-https://reviews.freebsd.org/D15540

Add upstream patch to fix the build with Qt 5.10.

    _tmp/ui/ui_Bowtie2Settings.h:189:35: error: no viable conversion from
'QLatin1String' to 'const QKeySequence'
            gbarCheckBox->setShortcut(QLatin1String(""));
                                      ^~~~~~~~~~~~~~~~~

PR:		228213

Update Qt5 ports to 5.9.3.

This took quite a lot of time because Qt's own build system underwent
several changes in 5.8.0 that took a while to adapt to.

And, of course, qt5-webengine is a behemoth that we need to patch like crazy
due to its bundling of Chromium. In fact, most of the Chromium patches in
qt5-webengine have been imported with no changes from www/chromium@433510
("www/chromium: update to 56.0.2924.87").

New port: accessibility/qt5-speech

Bigger changes to Qt5 ports we had to make:
- Qt now allows using a configure.json file to define configuration options
  and specify configuration checks that can be done when qmake is invoked.

Remove USES=execinfo.

PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488

Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845

- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL

Approved by:	portmgr blanket

The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.

Mark as broken on arm64.

Approved by:	portmgr (tier-2 blanket)

During the exp-run in bug 208158, it was found that biology/ugene gives
errors with libc++ 3.8.0:

In file included from src/QScoreAdapter.cpp:1:
In file included from src/QScoreAdapter.h:4:
In file included from ../../include/U2Core/MAlignment.h:1:
In file included from
../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25:
In file included from
../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25:
In file included from /usr/local/include/qt5/QtCore/QString:1:
In file included from /usr/local/include/qt5/QtCore/qstring.h:41:
In file included from /usr/local/include/qt5/QtCore/qchar.h:37:
In file included from /usr/local/include/qt5/QtCore/qglobal.h:39:
/usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found
#include_next <stddef.h>
              ^

This is because the port tries to add /usr/include as a system include
directory, using -isystem, and this screws up the order of include
directories.  Fix it by patching up a number of .pri files to avoid
using the -isystem flag.

Approved by:	h2+fbsdports@fsfe.org (maintainer)
PR:		209366
MFH:		2016Q2

Update to version 1.22.0, which now unfortunately requires Qt 5.x.  Also
since around v1.18.0, UGENE is using Google's Breakpad library for crash
reporting, which is very system-specific and does not support FreeBSD at
the moment.  Due to lack of resources and interest in porting it, simply
disable crash reporting code for the time being.

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

biology/ugene: qt4-linguist -> qt4-linguisttools

- add USES=desktop-file-utils

PR:                  202138
Submitted by:        s3erios@gmail.com
Approved by:         h2+fbsdports@fsfe.org

- Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)
- Remove no longer required local source code tweaks (picked up upstream)

Update Unipro UGENE to version 1.16.2.

- Update to version 1.16.1
- Explicitly list all required Qt components in USE_QT4 instead of relying
  on them being silently picked up through `www/webkit-qt4' dependency
- Group *_build components together while here
- Remove one REINPLACE_CMD call that is no longer needed

Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).

Update to version 1.15.1.

Update to version 1.15.0.

Cleanup plist

Update to version 1.14.2.

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

- Update Unipro UGENE and documentation to version 1.14.0
- Remove patches integrated upstream (it's nice to have direct contact)
- Sort USES and pkg-plist, cleanup Makefile a bit while here

Approved by:	maintainer (implicit)

USES=execinfo

Update to version 1.13.1.

Unbreak the fetch: one of the documentation PDF files was rerolled.

- Mark BROKEN because it does not fetch

- Update to version 1.13.0 and improve FreeBSD support; it also builds
  pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
  and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
  sanity checking tools; instead, list the docs explicitly in DISTFILES
  and add them to pkg-plist (guarded by %%PORTDOCS%%)

Tested on:	i386 (only)

- Install official UGENE documentation (PDF)
- Utilize DIST_SUBDIR as now it's more than one distfile

- Update to version 1.12.3
- Conditionalize dependency on `devel/libexecinfo'
- Try to detect SSE2 support
- Convert to USES=qmake and stafigy
- Improve grammar in port description while here

Approved by:	maintainer (implicit)

- Remove manual creation and removal of share/applications, as it's now in the
mtree (categories starting with [bce])

Approved by:	portmgr (bdrewery)

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)

Unbreak on 7.X and i386 systems.

Reported by:	QAT

Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell