Index: head/biology/ugene/Makefile =================================================================== --- head/biology/ugene/Makefile (revision 414783) +++ head/biology/ugene/Makefile (revision 414784) @@ -1,77 +1,78 @@ # Created by: Hannes Hauswedell # $FreeBSD$ PORTNAME= ugene DISTVERSION= 1.22.0 +PORTREVISION= 1 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 LICENSE= GPLv2 RUN_DEPENDS= bash:shells/bash USES= desktop-file-utils execinfo qmake USE_GL= glu USE_QT5= buildtools_build linguisttools_build scripttools_build \ gui network printsupport script sql svg webkit widgets xml \ imageformats_run QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \ INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \ LUPDATE="${LUPDATE}" ALL_TARGET= release DOCSDIR= ${DATADIR}/manuals OPTIONS_DEFINE= DOCS DOCS_DESC= Install official UGENE documentation (PDF) .include # Required for Google Test code .if ${OSVERSION} > 1000054 CXXFLAGS+= -std=c++11 .endif .if ${ARCH} == amd64 # XXX: need to manually tell the build we are on x64 QMAKE_ARGS+= CONFIG+=x64 PLIST_SUB+= NOX64="@comment " .else PLIST_SUB+= NOX64="" .endif .if ${MACHINE_CPU:Msse2} QMAKE_ARGS+= UGENE_SSE2_DETECTED=1 PLIST_SUB+= SSE2="" .else PLIST_SUB+= SSE2="@comment " .endif post-extract: @${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|' \ ${WRKSRC}/src/gen_bin_script.cmd \ ${WRKSRC}/installer/_common_data/ugene @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp @${REINPLACE_CMD} -e '/unix_not_mac/,+11d' \ ${WRKSRC}/src/corelibs/U2Core/U2Core.pri @${REINPLACE_CMD} 's, -lbreakpad,,' \ ${WRKSRC}/src/corelibs/U2Private/U2Private.pri \ ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ ${WRKSRC}/src/ugenecl/ugenecl.pri \ ${WRKSRC}/src/ugeneui/ugeneui.pri .include Index: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri =================================================================== --- head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (nonexistent) +++ head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (revision 414784) @@ -0,0 +1,11 @@ +--- src/libs_3rdparty/samtools/samtools.pri.orig 2016-03-31 12:21:56 UTC ++++ src/libs_3rdparty/samtools/samtools.pri +@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = '' + + TEMPLATE = lib + CONFIG +=thread debug_and_release staticlib warn_off +-INCLUDEPATH += src src/samtools ../../include /usr/include ++INCLUDEPATH += src src/samtools ../../include + win32 : INCLUDEPATH += src/samtools/win32 + DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE + win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca" Property changes on: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri =================================================================== --- head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (nonexistent) +++ head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (revision 414784) @@ -0,0 +1,11 @@ +--- src/plugins_3rdparty/variants/variants.pri.orig 2016-03-31 12:22:09 UTC ++++ src/plugins_3rdparty/variants/variants.pri +@@ -20,7 +20,7 @@ use_bundled_zlib() { + win32 : LIBS += -lwsock32 + + +-INCLUDEPATH += src ../../include /usr/include ++INCLUDEPATH += src ../../include + INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools + INCLUDEPATH += ../../libs_3rdparty/samtools/src + INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools Property changes on: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/ugene/files/patch-src_ugene__globals.pri =================================================================== --- head/biology/ugene/files/patch-src_ugene__globals.pri (nonexistent) +++ head/biology/ugene/files/patch-src_ugene__globals.pri (revision 414784) @@ -0,0 +1,13 @@ +--- src/ugene_globals.pri.orig 2016-03-31 12:22:21 UTC ++++ src/ugene_globals.pri +@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA + DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR} + DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH} + +-unix : !macx : INCLUDEPATH-=/usr/include +-unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include ++#unix : !macx : INCLUDEPATH-=/usr/include ++#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include + #unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH + + # NGS package Property changes on: head/biology/ugene/files/patch-src_ugene__globals.pri ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property