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-rw-r--r--academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch24
1 files changed, 24 insertions, 0 deletions
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