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