Date: Sun, 10 May 2020 15:42:33 +0000 (UTC) From: Alexey Dokuchaev <danfe@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r534852 - in head: . biology biology/ugene biology/ugene/files Message-ID: <202005101542.04AFgXYb034653@repo.freebsd.org>
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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Log: - Resurrect and unbreak by updating to version 34.0 - Stop providing outdated offline PDF documentation, users are advised to use the online files instead Added: head/biology/ugene/ - copied from r534092, head/biology/ugene/ Deleted: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@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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