From e036be1c887311811eb508fd0d49c41249e7c4fd Mon Sep 17 00:00:00 2001 From: Matteo Bernardini Date: Mon, 24 Sep 2018 22:20:22 +0200 Subject: 20180924.1 global branch merge. Signed-off-by: Matteo Bernardini --- .../ugene-1.22.0-dont_hardcode_includes.patch | 24 ++++++++++++++++++++++ academic/ugene/ugene.SlackBuild | 3 +++ 2 files changed, 27 insertions(+) create mode 100644 academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch (limited to 'academic/ugene') diff --git a/academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch b/academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch new file mode 100644 index 0000000000..6bc26e1f19 --- /dev/null +++ b/academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch @@ -0,0 +1,24 @@ +diff -up ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri +--- ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes 2016-03-31 07:21:56.000000000 -0500 ++++ ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri 2016-06-02 17:49:02.383069490 -0500 +@@ -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" +diff -up ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri +--- ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes 2016-03-31 07:22:09.000000000 -0500 ++++ ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri 2016-06-02 20:26:35.265356432 -0500 +@@ -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 diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index 058e03b6b8..e039fb7c11 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -73,6 +73,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# Thanks fedora +patch -p1 < $CWD/ugene-1.22.0-dont_hardcode_includes.patch + # Fix libraries and man pages paths sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri sed -i "s:/share/man:/man:g" src/ugene_globals.pri -- cgit v1.2.3