svn commit: r534852 - in head: . biology biology/ugene biology/ugene/files

Alexey Dokuchaev danfe at FreeBSD.org
Sun May 10 15:42:34 UTC 2020 

Author: danfe
Date: Sun May 10 15:42:32 2020
New Revision: 534852
URL: https://svnweb.freebsd.org/changeset/ports/534852

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  - Stop providing outdated offline PDF documentation,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

Added:
  head/biology/ugene/
     - copied from r534092, head/biology/ugene/
Deleted:
  head/biology/ugene/files/patch-git_578c949
  head/biology/ugene/files/patch-src_plugins_test__runner_src_Reporter.ui
Modified:
  head/MOVED
  head/biology/Makefile
  head/biology/ugene/Makefile
  head/biology/ugene/distinfo
  head/biology/ugene/pkg-plist

Modified: head/MOVED
==============================================================================
--- head/MOVED	Sun May 10 13:56:17 2020	(r534851)
+++ head/MOVED	Sun May 10 15:42:32 2020	(r534852)
@@ -14565,7 +14565,6 @@ biology/consed||2020-05-05|Has expired: Broken for mor
 biology/plinkseq||2020-05-05|Has expired: Broken for more than 6 months
 biology/seqtools||2020-05-05|Has expired: Broken for more than 6 months
 biology/t_coffee||2020-05-05|Has expired: Broken for more than 6 months
-biology/ugene||2020-05-05|Has expired: Broken for more than 6 months
 comms/ath3k-firmware||2020-05-05|Has expired: Broken for more than 6 months
 comms/geoid||2020-05-05|Has expired: Broken for more than 6 months
 comms/jerm||2020-05-05|Has expired: Broken for more than 6 months

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sun May 10 13:56:17 2020	(r534851)
+++ head/biology/Makefile	Sun May 10 15:42:32 2020	(r534852)
@@ -162,6 +162,7 @@
     SUBDIR += treepuzzle
     SUBDIR += trimadap
     SUBDIR += trimmomatic
+    SUBDIR += ugene
     SUBDIR += vcflib
     SUBDIR += vcftools
     SUBDIR += velvet

Modified: head/biology/ugene/Makefile
==============================================================================
--- head/biology/ugene/Makefile	Tue May  5 15:22:17 2020	(r534092)
+++ head/biology/ugene/Makefile	Sun May 10 15:42:32 2020	(r534852)
@@ -2,22 +2,12 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.31.0
-PORTREVISION=	1
+PORTVERSION=	34.0
 CATEGORIES=	biology science
-MASTER_SITES=	http://ugene.unipro.ru/downloads/
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
-		UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
-DIST_SUBDIR=	${PORTNAME}
-EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
 MAINTAINER=	h2+fbsdports at fsfe.org
 COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
 
-BROKEN=		unfetchable
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2020-05-05
-
 LICENSE=	GPLv2+
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
@@ -25,11 +15,15 @@ RUN_DEPENDS=	bash:shells/bash
 
 BROKEN_aarch64=	Fails to build: invokes x86 asm
 
+USE_GITHUB=	yes
+GH_ACCOUNT=	ugeneunipro
+
 USES=		desktop-file-utils gl qmake qt:5 shared-mime-info xorg
 USE_GL=		gl glu
 USE_QT=		buildtools_build linguisttools_build \
-		core gui network opengl printsupport script scripttools \
-		sql svg testlib webkit widgets xml \
+		core declarative gui opengl location network printsupport \
+		script scripttools sql svg testlib webchannel webengine \
+		websockets widgets xml \
 		imageformats_run
 USE_XORG=	x11 xtst
 
@@ -38,11 +32,8 @@ QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_D
 		LUPDATE="${LUPDATE}"
 ALL_TARGET=	release
 
-DOCSDIR=	${DATADIR}/manuals
+OPTIONS_DEFINE=	OPENCL
 
-OPTIONS_DEFINE=	DOCS OPENCL
-DOCS_DESC=	Install official UGENE documentation (PDF)
-
 OPENCL_QMAKE_ON=	UGENE_OPENCL_DETECTED=1
 
 .include <bsd.port.pre.mk>
@@ -56,10 +47,6 @@ QMAKE_ARGS+=	CONFIG+=x64
 QMAKE_ARGS+=	UGENE_SSE2_DETECTED=1
 .endif
 
-post-extract:
-	@${MKDIR} ${WRKSRC}/data/manuals
-	${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals
-
 post-patch:
 # yes, bash is required, stuff will not execute with sh
 	@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
@@ -67,10 +54,12 @@ post-patch:
 		${WRKSRC}/installer/_common_data/ugene
 	@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \
 		${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
-	@${REINPLACE_CMD} 's, -lbreakpad,,' \
+	@${REINPLACE_CMD} 's, -lbreakpad$$$$D,,' \
 		${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
 		${WRKSRC}/src/plugins_checker/plugins_checker.pri \
 		${WRKSRC}/src/ugenecl/ugenecl.pri \
 		${WRKSRC}/src/ugeneui/ugeneui.pri
+	@${REINPLACE_CMD} -e '422s|NULL|0|' \
+		${WRKSRC}/src/plugins/smith_waterman/src/SmithWatermanAlgorithmOPENCL.cpp
 
 .include <bsd.port.post.mk>

Modified: head/biology/ugene/distinfo
==============================================================================
--- head/biology/ugene/distinfo	Tue May  5 15:22:17 2020	(r534092)
+++ head/biology/ugene/distinfo	Sun May 10 15:42:32 2020	(r534852)
@@ -1,9 +1,3 @@
-TIMESTAMP = 1535840965
-SHA256 (ugene/ugene-1.31.0.tar.gz) = d1f46306834a292618cc54b31060b69da5b0b18da311a55bf82ab42f5a434320
-SIZE (ugene/ugene-1.31.0.tar.gz) = 20656562
-SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
-SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
-SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6
-SIZE (ugene/UniproUGENE_UserManual.pdf) = 13443754
-SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 8cc6630f62c82de42926c14c3d01ebc3c7d85ab7d9ec2a81e55a19740806735c
-SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29474484
+TIMESTAMP = 1584963065
+SHA256 (ugeneunipro-ugene-34.0_GH0.tar.gz) = 569b9997497680412e03d821c7d48903830012a65c5899a5aea3cb80e9f4ee25
+SIZE (ugeneunipro-ugene-34.0_GH0.tar.gz) = 23406266

Modified: head/biology/ugene/pkg-plist
==============================================================================
--- head/biology/ugene/pkg-plist	Tue May  5 15:22:17 2020	(r534092)
+++ head/biology/ugene/pkg-plist	Sun May 10 15:42:32 2020	(r534852)
@@ -1,8 +1,4 @@
 bin/ugene
-lib/ugene/libQSpec.so
-lib/ugene/libQSpec.so.1
-lib/ugene/libQSpec.so.1.0
-lib/ugene/libQSpec.so.1.0.0
 lib/ugene/libU2Algorithm.so
 lib/ugene/libU2Algorithm.so.1
 lib/ugene/libU2Algorithm.so.1.0
@@ -49,8 +45,6 @@ lib/ugene/libugenedb.so.1.0
 lib/ugene/libugenedb.so.1.0.0
 lib/ugene/plugins/CoreTests.license
 lib/ugene/plugins/CoreTests.plugin
-lib/ugene/plugins/GUITestBase.license
-lib/ugene/plugins/GUITestBase.plugin
 lib/ugene/plugins/annotator.license
 lib/ugene/plugins/annotator.plugin
 lib/ugene/plugins/api_tests.license
@@ -59,8 +53,6 @@ lib/ugene/plugins/ball.license
 lib/ugene/plugins/ball.plugin
 lib/ugene/plugins/biostruct3d_view.license
 lib/ugene/plugins/biostruct3d_view.plugin
-lib/ugene/plugins/browser_support.license
-lib/ugene/plugins/browser_support.plugin
 lib/ugene/plugins/chroma_view.license
 lib/ugene/plugins/chroma_view.plugin
 lib/ugene/plugins/circular_view.license
@@ -99,10 +91,6 @@ lib/ugene/plugins/libCoreTests.so
 lib/ugene/plugins/libCoreTests.so.1
 lib/ugene/plugins/libCoreTests.so.1.0
 lib/ugene/plugins/libCoreTests.so.1.0.0
-lib/ugene/plugins/libGUITestBase.so
-lib/ugene/plugins/libGUITestBase.so.1
-lib/ugene/plugins/libGUITestBase.so.1.0
-lib/ugene/plugins/libGUITestBase.so.1.0.0
 lib/ugene/plugins/libannotator.so
 lib/ugene/plugins/libannotator.so.1
 lib/ugene/plugins/libannotator.so.1.0
@@ -119,10 +107,6 @@ lib/ugene/plugins/libbiostruct3d_view.so
 lib/ugene/plugins/libbiostruct3d_view.so.1
 lib/ugene/plugins/libbiostruct3d_view.so.1.0
 lib/ugene/plugins/libbiostruct3d_view.so.1.0.0
-lib/ugene/plugins/libbrowser_support.so
-lib/ugene/plugins/libbrowser_support.so.1
-lib/ugene/plugins/libbrowser_support.so.1.0
-lib/ugene/plugins/libbrowser_support.so.1.0.0
 lib/ugene/plugins/libchroma_view.so
 lib/ugene/plugins/libchroma_view.so.1
 lib/ugene/plugins/libchroma_view.so.1.0
@@ -195,6 +179,10 @@ lib/ugene/plugins/liblinkdata_support.so
 lib/ugene/plugins/liblinkdata_support.so.1
 lib/ugene/plugins/liblinkdata_support.so.1.0
 lib/ugene/plugins/liblinkdata_support.so.1.0.0
+lib/ugene/plugins/libmetaphlan2_support.so
+lib/ugene/plugins/libmetaphlan2_support.so.1
+lib/ugene/plugins/libmetaphlan2_support.so.1.0
+lib/ugene/plugins/libmetaphlan2_support.so.1.0.0
 lib/ugene/plugins/libngs_reads_classification.so
 lib/ugene/plugins/libngs_reads_classification.so.1
 lib/ugene/plugins/libngs_reads_classification.so.1.0
@@ -277,6 +265,8 @@ lib/ugene/plugins/libworkflow_designer.so.1.0
 lib/ugene/plugins/libworkflow_designer.so.1.0.0
 lib/ugene/plugins/linkdata_support.license
 lib/ugene/plugins/linkdata_support.plugin
+lib/ugene/plugins/metaphlan2_support.license
+lib/ugene/plugins/metaphlan2_support.plugin
 lib/ugene/plugins/ngs_reads_classification.license
 lib/ugene/plugins/ngs_reads_classification.plugin
 lib/ugene/plugins/opencl_support.license
@@ -402,7 +392,6 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/hmm3-build-and-search.uwl
 %%DATADIR%%/cmdline/join-quality.uwl
 %%DATADIR%%/cmdline/local-blast+.uwl
-%%DATADIR%%/cmdline/local-blast.uwl
 %%DATADIR%%/cmdline/pfm-build.uwl
 %%DATADIR%%/cmdline/pfm-search.uwl
 %%DATADIR%%/cmdline/pwm-build.uwl
@@ -424,9 +413,6 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/genome_lengths/mm9.genome
 %%DATADIR%%/genome_lengths/test.genome
 %%DATADIR%%/license
-%%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf
-%%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf
-%%PORTDOCS%%%%DOCSDIR%%/WorkflowDesigner_UserManual.pdf
 %%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm

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