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-rw-r--r--sci-biology/mummer/Manifest8
-rw-r--r--sci-biology/mummer/files/mummer-3.23-fix-build-system.patch397
-rw-r--r--sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch83
-rw-r--r--sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch75
-rw-r--r--sci-biology/mummer/metadata.xml11
-rw-r--r--sci-biology/mummer/mummer-3.23.ebuild46
6 files changed, 620 insertions, 0 deletions
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
new file mode 100644
index 000000000000..e1ee929f6519
--- /dev/null
+++ b/sci-biology/mummer/Manifest
@@ -0,0 +1,8 @@
+AUX mummer-3.23-fix-build-system.patch 10130 SHA256 4cb6a96d68713039b8edf796960bcd5adf00751869acbbe12b377f5cf1176b81 SHA512 4979c8ab1fde7a134e2feb5a758fbd1b9fe125e056e53f09ea620183d9b2492452cd8be473e474c8a88e4a25acbd7e20d401146c38cbedee564a03a601f92ca0 WHIRLPOOL 86d31520296191005c05b0f82a66ca05af91d5d7db75622faec6c26b717b603cd24f7fd171c1dda4619efee4b45006dafe7d41f488dcf63aa714fc7ce443c2e4
+AUX mummer-3.23-fix-c++-qa.patch 2615 SHA256 99acb89564439528b30f64448c193cd8302e58c7503b5d87074301bf2e712e42 SHA512 ca1a8156ecac367817f4678ed9fd0dd7e5f31cce0d8d167dd9245ea1e2ad4b4acad254277483f99764891a0cbad8ca6f879acc731b8e3e306e5644739c0f82d2 WHIRLPOOL a72fb08be411694fa5050628a1825050fe364243db8ee1d774e8ac3a7e02d0f8ad5937f607d314e4d84abf18481e2a25f52b8e2835385a077b48312bce792544
+AUX mummer-3.23-fix-shebangs.patch 2357 SHA256 1307243770f1af4aa508a00715d29b571b169807aa0102d8ec30af7becef335e SHA512 d0ac58170232244385328d3a23e6b8203593d32dda30d75915b4da8ad935fc1dc447b2a7c7d982b0a86c9fe4ca6f8c2031fe7f81af8a72bfba4d56ae6d246235 WHIRLPOOL 3c3fbbe2b99cda779283a9d9dc0b4b586c98dc1ba213be2c1007e9f170d80f72c4c253e599824aed2f8607c815f614619955f8b79d75778e9c34265f570f49c1
+DIST MUMmer3.23.tar.gz 3160143 SHA256 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 WHIRLPOOL 7471d20a88f5ddf510d1e4826480706a683f005f3bab21ebb19b1fcba2c8f431435cce27a1cdf98ece8d4bb4dafcc349362037f6d526db3f564b7c013c67e882
+EBUILD mummer-3.23.ebuild 1133 SHA256 da065cb1a4314c709fb6fcac8a2079dcfb31664cd7b3430e19071e609ec9d6f8 SHA512 a25b94cb5e7a8261178d0a503c33812f106dde277c94a8525a0a8fcd6c120ec6b0d5cb80f26f0710245f89251ad4ac6e4fe86af42f31b31f37ab9eca6afc3b79 WHIRLPOOL 205e432b5a3c915913f15ebbe2ee2710e85a54ff1967ad26a4459a4f8c599fd828abea6813439c61d5d5e71884dd09603693e3d8facb3028b56b6b2cf753dd08
+MISC ChangeLog 2614 SHA256 c419c030871bff1d34b413648db36e3d476ecda28b88cb145925695b144661da SHA512 11b57a837714ea4725b07e0d3b5e09c621c40d7a362705a346d2562868d525eec054ae74147d07095f3e0c19cf865295ba1938743b2ddceae4371644ff029f8b WHIRLPOOL 4bbe42eaf6eed492df2ab6d192d8e7c29fe78cad9648c9cca9c1266f3267349cb5dee61b755d6a8ffb6b6278ba956ce342b4a82cfa10fb6b2aa8092d08ac75c1
+MISC ChangeLog-2015 2204 SHA256 6ba244dff6d066d6365eb4eb986cbc76f93015f16de562b2cabcb6e07805ac8e SHA512 b5c4554ef2cdc436db529a2122558857549683c7742e8a47cc8fcf01e1aa833036d4f6797fd5e8dc2339a44052a20e075b2aacb9e991757271c63dbf7d6bf392 WHIRLPOOL f33a5caa560957d50597daf1ff5bdccfd122378e24e5288bc0d3b592ea30e970332eb67df76377fb7c2186a64a2ab441b3127e8b0a67babd7dfff2cdf9f26802
+MISC metadata.xml 347 SHA256 090b02afe3d221595404585ab81794b7200d2debc18bbd87778a420e2c93bd9b SHA512 7465b510db1cbf2b5853452e947585e6526068aaa0562b7e3ad415838d97ecf30cf32967997c16bab17ac9c41921c0f92dc2a9647fde402f448d6f6dc1d2244c WHIRLPOOL e02461914ac5c1b2607dd7429486e9e0a0ccfbce3cc7e1543af724dd57a43660a974b6050a797123be01eefea593a8ed8277a983dece07708914e3c2829c7e96
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch
new file mode 100644
index 000000000000..b92f75c07719
--- /dev/null
+++ b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch
@@ -0,0 +1,397 @@
+Fix build system to restore some sanity
+
+--- a/Makefile
++++ b/Makefile
+@@ -27,31 +27,27 @@
+
+
+ TOP_DIR := $(CURDIR)
+-BIN_DIR := $(TOP_DIR)
+-AUX_BIN_DIR := $(TOP_DIR)/aux_bin
++
++BIN_DIR = $(EPREFIX)/usr/bin
++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts
++AUX_BIN_DIR = $(EPREFIX)/usr/bin
+
+ DOC_DIR := $(TOP_DIR)/docs
+ SCRIPT_DIR := $(TOP_DIR)/scripts
+ TIGR_SRC_DIR := $(TOP_DIR)/src/tigr
+ KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
+
+-CC := $(filter /%,$(shell /bin/sh -c 'type gcc'))
+-CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))
+ SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
+ CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+-AR := $(filter /%,$(shell /bin/sh -c 'type ar'))
+
+-CXXFLAGS = -O3
+-CFLAGS = -O3
+-LDFLAGS =
+
+ FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
+
+
+
+ #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
+-export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
++export BIN_DIR SCRIPT_DIR AUX_BIN_DIR
+
+
+
+@@ -114,15 +110,15 @@
+
+
+ kurtz:
+- cd $(KURTZ_SRC_DIR); $(MAKE) mummer
++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer
+
+
+ scripts:
+- cd $(SCRIPT_DIR); $(MAKE) all
++ $(MAKE) -C $(SCRIPT_DIR) all
+
+
+ tigr:
+- cd $(TIGR_SRC_DIR); $(MAKE) all
++ $(MAKE) -C $(TIGR_SRC_DIR) all
+
+
+ uninstall: clean
+--- a/scripts/Makefile
++++ b/scripts/Makefile
+@@ -1,21 +1,10 @@
+-#-- Imported variables from top level makefile
+-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
++BIN_DIR = $(EPREFIX)/usr/bin
++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts
++AUX_BIN_DIR = $(EPREFIX)/usr/bin
+
+-ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
+-endif
+-ifndef AUX_BIN_DIR
+-AUX_BIN_DIR := $(CURDIR)
+-endif
+-ifndef SCRIPT_DIR
+-SCRIPT_DIR := $(CURDIR)
+-endif
+-
+-SCRIPT_DIR := $(CURDIR)
+ SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
+ CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+-VPATH := $(BIN_DIR)
+
+ ALL := exact-tandems mapview mummerplot nucmer promer \
+ run-mummer1 run-mummer3 nucmer2xfig dnadiff
+@@ -39,58 +28,49 @@
+ $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- exact-tandems.csh > $(BIN_DIR)/exact-tandems
+- chmod 755 $(BIN_DIR)/exact-tandems
++ exact-tandems.csh > exact-tandems
+
+ mapview: mapview.pl
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- mapview.pl > $(BIN_DIR)/mapview
+- chmod 755 $(BIN_DIR)/mapview
++ mapview.pl > mapview
+
+ mummerplot: mummerplot.pl Foundation.pm
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- mummerplot.pl > $(BIN_DIR)/mummerplot
+- chmod 755 $(BIN_DIR)/mummerplot
++ mummerplot.pl > mummerplot
+
+ dnadiff: dnadiff.pl Foundation.pm
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- dnadiff.pl > $(BIN_DIR)/dnadiff
+- chmod 755 $(BIN_DIR)/dnadiff
++ dnadiff.pl > dnadiff
+
+ nucmer: nucmer.pl Foundation.pm
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+ -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- nucmer.pl > $(BIN_DIR)/nucmer
+- chmod 755 $(BIN_DIR)/nucmer
++ nucmer.pl > nucmer
+
+ promer: promer.pl Foundation.pm
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+ -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- promer.pl > $(BIN_DIR)/promer
+- chmod 755 $(BIN_DIR)/promer
++ promer.pl > promer
+
+ run-mummer1: run-mummer1.csh
+ $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- run-mummer1.csh > $(BIN_DIR)/run-mummer1
+- chmod 755 $(BIN_DIR)/run-mummer1
++ run-mummer1.csh > run-mummer1
+
+ run-mummer3: run-mummer3.csh
+ $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- run-mummer3.csh > $(BIN_DIR)/run-mummer3
+- chmod 755 $(BIN_DIR)/run-mummer3
++ run-mummer3.csh > run-mummer3
+
+ nucmer2xfig: nucmer2xfig.pl
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+- nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
+- chmod 755 $(BIN_DIR)/nucmer2xfig
++ nucmer2xfig.pl > nucmer2xfig
+--- a/src/kurtz/libbasedir/Makefile
++++ b/src/kurtz/libbasedir/Makefile
+@@ -5,8 +5,6 @@
+
+ SPLINTFLAGS=-f ../Splintoptions -DDEBUG
+
+-LD=$(CC)
+-
+ ##CFLAGS=${DEFINECFLAGS}
+
+ LIBBASE=libbase.a
+@@ -24,14 +22,14 @@
+
+
+ $(LIBBASE): $(LIBOBJECTS)
+- ar sruv $@ $(LIBOBJECTS)
++ $(AR) sruv $@ $(LIBOBJECTS)
+
+
+ include Filegoals.mf
+
+
+ $(LIBBASEDBG): $(LIBDEBUGOBJECTS)
+- ar sruv $@ $(LIBDEBUGOBJECTS)
++ $(AR) sruv $@ $(LIBDEBUGOBJECTS)
+
+
+ .PHONY:clean
+--- a/src/kurtz/Makefile
++++ b/src/kurtz/Makefile
+@@ -1,7 +1,7 @@
+ all:
+- cd libbasedir; $(MAKE) all
+- cd streesrc; $(MAKE) all
+- cd mm3src; $(MAKE) all
++ $(MAKE) -C libbasedir all
++ $(MAKE) -C streesrc all
++ $(MAKE) -C mm3src all
+
+ clean:
+ rm -f *~
+@@ -10,11 +10,11 @@
+ cd mm3src; $(MAKE) clean
+
+ mummer:
+- cd libbasedir; $(MAKE) libbase.a
+- cd streesrc; $(MAKE) libstree.a
+- cd mm3src; $(MAKE) mummer
++ $(MAKE) -C libbasedir libbase.a
++ $(MAKE) -C streesrc libstree.a
++ $(MAKE) -C mm3src mummer
+
+ splintall:
+- cd libbasedir; ${MAKE} splintall
+- cd streesrc; ${MAKE} splintall
+- cd mm3src; ${MAKE} splintall
++ $(MAKE) -C libbasedir splintall
++ $(MAKE) -C streesrc splintall
++ $(MAKE) -C mm3src splintall
+--- a/src/kurtz/mm3src/Makefile
++++ b/src/kurtz/mm3src/Makefile
+@@ -3,11 +3,7 @@
+
+ ##include ../Makedef
+
+-ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
+-endif
+-
+-VPATH := $(BIN_DIR)
++BIN_DIR = $(EPREFIX)/usr/bin
+
+ ALL := maxmat3.x maxmat3.dbg.x
+
+@@ -15,11 +11,8 @@
+ LIBSTREEDIR=../streesrc
+ INCLUDEDIR=-I${LIBBASEDIR} -I${LIBSTREEDIR}
+
+-override CFLAGS+=$(INCLUDEDIR)
+-##CFLAGS=${DEFINECFLAGS} $(INCLUDEDIR)
+-##LDFLAGS=${DEFINELDFLAGS}
++override CPPFLAGS+=$(INCLUDEDIR)
+ SPLINTFLAGS=${INCLUDEDIR} -f ../Splintoptions -DDEBUG
+-LD=$(CC)
+
+ LIBBASE=$(LIBBASEDIR)/libbase.a
+ LIBBASEDBG=$(LIBBASEDIR)/libbase.dbg.a
+@@ -40,16 +33,16 @@
+ all: $(ALL)
+
+ mummer: $(MUM3OBJECTS) $(LIBSTREE)
+- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
++ -o $@
+
+ maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
+- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
++ -o $@
+
+ maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
+- $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
+- -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++ $(CC) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
++ -lm -o $@
+
+ include Filegoals.mf
+
+--- a/src/kurtz/streesrc/Makefile
++++ b/src/kurtz/streesrc/Makefile
+@@ -23,8 +23,6 @@
+
+ #-DSTARTFACTOR=0.5
+
+-LD=${CC}
+-
+ LIBBASE=${LIBBASEDIR}/libbase.a
+ LIBBASEDBG=${LIBBASEDIR}/libbase.dbg.a
+
+@@ -65,29 +63,29 @@
+ include Filegoals.mf
+
+ libstree.4.a: $(OBJECTS4)
+- ar sruv $@ $(OBJECTS4)
++ $(AR) sruv $@ $(OBJECTS4)
+
+ libstree.a: $(OBJECTS)
+- ar sruv $@ $(OBJECTS)
++ $(AR) sruv $@ $(OBJECTS)
+
+ libstree.dbg.4.a: $(DBGOBJECTS4)
+- ar sruv $@ $(DBGOBJECTS4)
++ $(AR) sruv $@ $(DBGOBJECTS4)
+
+ libstree.dbg.a: $(DBGOBJECTS)
+- ar sruv $@ $(DBGOBJECTS)
++ $(AR) sruv $@ $(DBGOBJECTS)
+
+
+ stree.x: stree.o libstree.a
+- $(LD) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@
++ $(CC) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@
+
+ loc.x: loc.o libstree.a
+- $(LD) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@
++ $(CC) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@
+
+ stree.dbg.x: stree.dbg.o libstree.dbg.a
+- $(LD) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
++ $(CC) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
+
+ loc.dbg.x: loc.dbg.o libstree.dbg.a
+- $(LD) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
++ $(CC) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
+
+ streeproto.h: $(PROTOFILES) Mkstreeproto.sh
+ @echo "make $@"
+--- a/src/tigr/Makefile
++++ b/src/tigr/Makefile
+@@ -1,20 +1,3 @@
+-#-- Imported variables from top level makefile
+-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
+-
+-ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
+-endif
+-ifndef AUX_BIN_DIR
+-AUX_BIN_DIR := $(CURDIR)
+-endif
+-
+-OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
+-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
+- chmod 755 $(BIN_DIR)/$@
+-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
+- chmod 755 $(AUX_BIN_DIR)/$@
+-VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
+-
+ ALL := annotate combineMUMs delta-filter gaps mgaps \
+ postnuc postpro prenuc prepro repeat-match \
+ show-aligns show-coords show-tiling show-snps \
+@@ -38,59 +21,22 @@
+
+ #-- not so PHONY rules --#
+ delta.o: delta.cc delta.hh
+- $(OBJ_RULE)
+-
+ tigrinc.o: tigrinc.cc tigrinc.hh
+- $(OBJ_RULE)
+-
+ sw_align.o: sw_align.cc sw_align.hh tigrinc.hh
+- $(OBJ_RULE)
+-
+ translate.o: translate.cc translate.hh
+- $(OBJ_RULE)
+-
+
+ annotate: annotate.cc tigrinc.o
+- $(BIN_RULE)
+-
+ combineMUMs: combineMUMs.cc tigrinc.o
+- $(BIN_RULE)
+-
+ delta-filter: delta-filter.cc tigrinc.o delta.o
+- $(BIN_RULE)
+-
+ gaps: gaps.cc tigrinc.o
+- $(BIN_RULE)
+-
+ mgaps: mgaps.cc tigrinc.o
+- $(BIN_RULE)
+-
+ postnuc: postnuc.cc tigrinc.o sw_align.o
+- $(AUX_BIN_RULE)
+-
+ postpro: postpro.cc tigrinc.o sw_align.o translate.o
+- $(AUX_BIN_RULE)
+-
+ prenuc: prenuc.cc tigrinc.o
+- $(AUX_BIN_RULE)
+-
+ prepro: prepro.cc tigrinc.o translate.o
+- $(AUX_BIN_RULE)
+-
+ repeat-match: repeat-match.cc tigrinc.o
+- $(BIN_RULE)
+-
+ show-aligns: show-aligns.cc tigrinc.o translate.o delta.o
+- $(BIN_RULE)
+-
+ show-coords: show-coords.cc tigrinc.o delta.o
+- $(BIN_RULE)
+-
+ show-tiling: show-tiling.cc tigrinc.o delta.o
+- $(BIN_RULE)
+-
+ show-snps: show-snps.cc tigrinc.o translate.o delta.o
+- $(BIN_RULE)
+-
+ show-diff: show-diff.cc tigrinc.o delta.o
+- $(BIN_RULE)
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch b/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch
new file mode 100644
index 000000000000..d6926c913d4a
--- /dev/null
+++ b/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch
@@ -0,0 +1,83 @@
+--- a/src/kurtz/libbasedir/space.c
++++ b/src/kurtz/libbasedir/space.c
+@@ -379,7 +379,7 @@
+ }
+ if(numberofblocks > 0)
+ {
+- fprintf(stderr,"space leak: number of blocks = %u\n",numberofblocks);
++ fprintf(stderr,"space leak: number of blocks = %lu\n",numberofblocks);
+ exit(EXIT_FAILURE);
+ }
+ free(blocks);
+--- a/src/tigr/combineMUMs.cc
++++ b/src/tigr/combineMUMs.cc
+@@ -106,7 +106,7 @@
+ // This array [i] is the maximum number of errors allowed
+ // in a match between sequences of length i , which is
+ // i * MAXERROR_RATE .
+-char * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
++const char * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
+ // Name of file to write gaps listing with # errors in each gap
+ int Fill_Ct = 0;
+ // Number of non-acgt bases in ref sequence
+@@ -132,7 +132,7 @@
+ // The query sequence
+ long int Query_Len;
+ // The length of the query sequence
+-char * Query_Suffix = "Query";
++const char * Query_Suffix = "Query";
+ // Suffix for query tag
+ char * Ref = NULL;
+ // The reference sequence
+@@ -142,7 +142,7 @@
+ // The length of the reference sequence
+ long int Ref_Size;
+ // The size of the reference sequence buffer
+-char * Ref_Suffix = "Ref";
++const char * Ref_Suffix = "Ref";
+ // Suffix for reference tag
+ int Show_Differences = FALSE;
+ // If TRUE then show differences in all alignments
+--- a/src/tigr/mgaps.cc
++++ b/src/tigr/mgaps.cc
+@@ -64,9 +64,9 @@
+ static void Parse_Command_Line
+ (int argc, char * argv []);
+ static void Process_Matches
+- (Match_t * A, int N, char * label);
++ (Match_t * A, int N, const char * label);
+ static int Process_Cluster
+- (Match_t * A, int N, char * label);
++ (Match_t * A, int N, const char * label);
+ static void Union
+ (int a, int b);
+ static void Usage
+@@ -438,7 +438,7 @@
+
+
+ static int Process_Cluster
+- (Match_t * A, int N, char * label)
++ (Match_t * A, int N, const char * label)
+
+ // Process the cluster of matches in A [0 .. (N - 1)] and output them
+ // after a line containing label . Return the number of clusters
+@@ -552,7 +552,7 @@
+
+
+ static void Process_Matches
+- (Match_t * A, int N, char * label)
++ (Match_t * A, int N, const char * label)
+
+ // Process matches A [1 .. N] and output them after
+ // a line containing label .
+--- a/src/tigr/show-coords.cc
++++ b/src/tigr/show-coords.cc
+@@ -788,7 +788,7 @@
+ (vector<AlignStats> Stats)
+ {
+ time_t currtime;
+- char * type;
++ const char * type;
+ char date[MAX_LINE];
+ long int len;
+ vector<AlignStats>::iterator Sip;
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch
new file mode 100644
index 000000000000..97f1dd843aca
--- /dev/null
+++ b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch
@@ -0,0 +1,75 @@
+Use portable shebangs instead of hardcoding interpreters
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
+
+--- a/scripts/dnadiff.pl
++++ b/scripts/dnadiff.pl
+@@ -1,4 +1,4 @@
+-#!__PERL_PATH -w
++#!/usr/bin/env perl
+
+ #-------------------------------------------------------------------------------
+ # Programmer: Adam M Phillippy, University of Maryland
+--- a/scripts/exact-tandems.csh
++++ b/scripts/exact-tandems.csh
+@@ -1,4 +1,4 @@
+-#!__CSH_PATH -f
++#!/usr/bin/env csh
+ #
+ # Find exact tandem repeats in specified file involving an
+ # exact duplicate of at least the specified length
+--- a/scripts/mapview.pl
++++ b/scripts/mapview.pl
+@@ -1,4 +1,4 @@
+-#!__PERL_PATH
++#!/usr/bin/env perl
+
+ use lib "__SCRIPT_DIR";
+ use Foundation;
+--- a/scripts/mummerplot.pl
++++ b/scripts/mummerplot.pl
+@@ -1,4 +1,4 @@
+-#!__PERL_PATH
++#!/usr/bin/env perl
+
+ ################################################################################
+ # Programmer: Adam M Phillippy, The Institute for Genomic Research
+--- a/scripts/nucmer2xfig.pl
++++ b/scripts/nucmer2xfig.pl
+@@ -1,4 +1,4 @@
+-#!__PERL_PATH
++#!/usr/bin/env perl
+ # (c) Steven Salzberg 2001
+ # Make an xfig plot for a comparison of a reference chromosome (or single
+ # molecule) versus a multifasta file of contigs from another genome.
+--- a/scripts/nucmer.pl
++++ b/scripts/nucmer.pl
+@@ -1,4 +1,4 @@
+-#!__PERL_PATH
++#!/usr/bin/env perl
+
+ #-------------------------------------------------------------------------------
+ # Programmer: Adam M Phillippy, The Institute for Genomic Research
+--- a/scripts/promer.pl
++++ b/scripts/promer.pl
+@@ -1,4 +1,4 @@
+-#!__PERL_PATH
++#!/usr/bin/env perl
+
+ #-------------------------------------------------------------------------------
+ # Programmer: Adam M Phillippy, The Institute for Genomic Research
+--- a/scripts/run-mummer1.csh
++++ b/scripts/run-mummer1.csh
+@@ -1,4 +1,4 @@
+-#!__CSH_PATH -f
++#!/usr/bin/env csh
+ #
+ # **SEVERELY** antiquated script for running the mummer 1 suite
+ # -r option reverse complements the query sequence, coordinates of the reverse
+--- a/scripts/run-mummer3.csh
++++ b/scripts/run-mummer3.csh
+@@ -1,4 +1,4 @@
+-#!__CSH_PATH -f
++#!/usr/bin/env csh
+ #
+ # for running the basic mummer 3 suite, should use nucmer instead when possible
+ # to avoid the confusing reverse coordinate system of the raw programs.
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
new file mode 100644
index 000000000000..4a3fe8e7bd15
--- /dev/null
+++ b/sci-biology/mummer/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">mummer</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mummer/mummer-3.23.ebuild b/sci-biology/mummer/mummer-3.23.ebuild
new file mode 100644
index 000000000000..4839053f4191
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.23.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="
+ app-shells/tcsh
+ dev-lang/perl"
+
+S=${WORKDIR}/MUMmer${PV}
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-3.23-fix-build-system.patch
+ "${FILESDIR}"/${PN}-3.23-fix-c++-qa.patch
+ "${FILESDIR}"/${PN}-3.23-fix-shebangs.patch
+)
+
+src_configure() {
+ use amd64 && append-cppflags -DSIXTYFOURBITS
+ tc-export AR CC CXX
+}
+
+src_install() {
+ dobin src/kurtz/mm3src/mummer
+ dobin src/tigr/{combineMUMs,delta-filter,gaps,mgaps,postnuc,postpro,prenuc,prepro,repeat-match,show-aligns,show-coords,show-tiling,show-snps,show-diff}
+ dobin scripts/{exact-tandems,mapview,mummerplot,dnadiff,nucmer,promer,run-mummer1,run-mummer3,nucmer2xfig}
+ newbin src/tigr/annotate mummer-annotate
+
+ insinto /usr/share/${PN}/lib
+ doins scripts/Foundation.pm
+
+ einstalldocs
+ use doc && dodoc -r docs/.
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-22 21:19:20 +0000