Commit cb8612e3 authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

update patches

parent fec27de4

debian/patches/debian-gt-libs.patch

+7 −6
Original line number Diff line number Diff line 
--- a/Makefile

+++ b/Makefile

@@ -15,19 +15,16 @@

@@ -15,19 +15,17 @@

 # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

 #
@@ -11,6 +11,7 @@ 
-            -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \

+INCLUDEOPT:=-I/usr/include/genometools \

+	    -I/usr/include/vmatch \

+	    -I/usr/include/lua5.1 \

             -I$(CURDIR)/src -I$(CURDIR)/obj \

 # these variables are exported by the configuration script

-CC:=gcc
@@ -24,7 +25,7 @@ 
 

 ifneq ($(fpic),no)

   FPIC:=-fPIC

@@ -130,11 +127,11 @@

@@ -130,11 +128,11 @@

 GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d)

 

 VSTREEDIR:=../vstree/src
@@ -41,7 +42,7 @@ 
 GTH_CPPFLAGS+=-I$(CURDIR)/$(VSTREEDIR)/include \

              -I$(CURDIR)/$(VSTREEDIR)/Vmatch \

 

@@ -209,7 +206,7 @@

@@ -209,7 +207,7 @@

 all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \

      bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \

      bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \
@@ -50,7 +51,7 @@ 
 

 lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)

 	@echo "[link $(@F)]"

@@ -231,67 +228,67 @@

@@ -231,67 +229,67 @@

 $(1): $(2)

 	@echo "[link $$(@F)]"

 	@test -d $$(@D) || mkdir -p $$(@D)
@@ -136,7 +137,7 @@ 
 

 obj/gth_config.h: VERSION

 	@echo '[create $@]'

@@ -321,9 +318,9 @@

@@ -321,9 +319,9 @@

 $(1): $(2)

 	@echo "[compile $$(@F)]"

 	@test -d $$(@D) || mkdir -p $$(@D)
@@ -148,7 +149,7 @@ 
         $(3) -MM -MP -MT $$@

 endef

 

@@ -332,17 +329,17 @@

@@ -332,17 +330,17 @@

 obj/%.o: %.cxx

 	@echo "[compile $(@F)]"

 	@test -d $(@D) || mkdir -p $(@D)

debian/patches/gt-path-fix.patch

+11 −0
Original line number Diff line number Diff line
@@ -307,3 +307,14 @@ 
              "#{$gthtestdata}ngasp/test_ref2.gff3 " +

              "#{$gthtestdata}ngasp/ngasp.gff3", :maxtime => 300

     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/ngasp.specificity"

--- a/Makefile

+++ b/Makefile

@@ -517,7 +517,7 @@

                           -gtdonor -agacceptor -gzip

 	@touch $@

 

-obj/old_train: ../genometools/bin/gt

+obj/old_train: bin/gthmkbssmfiles

 	@echo "[write old BSSMs]"

 	@bin/gthmkbssmfiles bin/bssm

 	@touch $@