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commit: 11d10cd16517dbbba9573653b1909995a4033571 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Wed Mar 8 21:35:39 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Wed Mar 8 22:15:49 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=11d10cd1 |
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|
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sci-biology/mummer: Version bump to 3.23 |
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|
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* EAPI 6 |
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* Make build system saner |
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* Fix C++ QA warnings |
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|
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Package-Manager: Portage-2.3.4, Repoman-2.3.2 |
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Closes: https://github.com/gentoo/gentoo/pull/4165 |
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|
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sci-biology/mummer/Manifest | 1 + |
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.../files/mummer-3.23-fix-build-system.patch | 397 +++++++++++++++++++++ |
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.../mummer/files/mummer-3.23-fix-c++-qa.patch | 83 +++++ |
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.../mummer/files/mummer-3.23-fix-shebangs.patch | 75 ++++ |
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sci-biology/mummer/mummer-3.23.ebuild | 46 +++ |
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5 files changed, 602 insertions(+) |
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|
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diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest |
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index 8089124a742..e752ce6907b 100644 |
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--- a/sci-biology/mummer/Manifest |
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+++ b/sci-biology/mummer/Manifest |
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@@ -1,4 +1,5 @@ |
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DIST MUMmer3.20.tar.gz 3155446 SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 SHA512 7c80bb605d57739809eb1b1cf8a579d72048e510362237d9ba64e21be18cc663769cda5dabc287832e59fb62804df34bc8336c2b42474466e7ee1e126848aecd WHIRLPOOL a08af35aee960bcd6274d3a00b1c1819d23367c81a72fd41c652c3579253b0aeeb5ef66f6dcfed60b4987c3a40830d04cd81745dce8a274cc3de0663dd54ae6f |
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DIST MUMmer3.21.tar.gz 3155965 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8 SHA512 61d49e5451e1697003f7acaac690f2ede7ab71766208d3218954527c48be76ddb78d60ff40ae1bdcd4b93d3efaf21b5bd027da3722eab1ae3fa399ee726bc96e WHIRLPOOL 50c7b0d7c00bf85aa8e0f8b80bf55186f8c0a53d26c3e50d2149120bc46f3632de4cb861a4d4265c1e3be731dffb71940344b238fd3e977412134b0e401cb95e |
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DIST MUMmer3.22.tar.gz 3156338 SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da SHA512 37bbb368c679d2e98fa9b9ef10c18008c173c25ee79183eb30e34125b1dc9cd10f005b7bd7c648335a8025509d8e3456fcc7ce497c95fa71c3c5d3ed3685665f WHIRLPOOL 487333ca38a9c59984ed059e8dd620ad3c0a5ae1a537e500c7b8b2d58213ac88960a13c0f25e6e0490d1209c9e73cfe8df0f8a43dbae9fd6a3e9fe3ce42da453 |
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+DIST MUMmer3.23.tar.gz 3160143 SHA256 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 WHIRLPOOL 7471d20a88f5ddf510d1e4826480706a683f005f3bab21ebb19b1fcba2c8f431435cce27a1cdf98ece8d4bb4dafcc349362037f6d526db3f564b7c013c67e882 |
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DIST mummer-3.9.4_alpha.tar.gz 956517 SHA256 fb2f03c729cd078d526d6318f91061f8832c2e8bd0d519ddf3c0b6e656029cfa SHA512 f0b962a69df6918afc7d163b30bcf5bd9eb2be663c8ac685b5e06317953cf12b9d240df8a5bfe8a9410b65cf88176cc7a71eecfc460e51df7ad1b27dc3a10fc2 WHIRLPOOL 8443cde87f868136eaa005db2b5b461a822097778d4c36448602a5cda058dc1dfa10daa08883248ffaba79a1d33240170b94b96548ebb56a01eaa27838d4afd6 |
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|
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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 |
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new file mode 100644 |
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index 00000000000..b92f75c0771 |
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--- /dev/null |
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+++ b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch |
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@@ -0,0 +1,397 @@ |
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+Fix build system to restore some sanity |
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+ |
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+--- a/Makefile |
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++++ b/Makefile |
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+@@ -27,31 +27,27 @@ |
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+ |
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+ |
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+ TOP_DIR := $(CURDIR) |
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+-BIN_DIR := $(TOP_DIR) |
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+-AUX_BIN_DIR := $(TOP_DIR)/aux_bin |
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++ |
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++BIN_DIR = $(EPREFIX)/usr/bin |
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++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts |
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++AUX_BIN_DIR = $(EPREFIX)/usr/bin |
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+ |
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+ DOC_DIR := $(TOP_DIR)/docs |
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+ SCRIPT_DIR := $(TOP_DIR)/scripts |
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+ TIGR_SRC_DIR := $(TOP_DIR)/src/tigr |
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+ KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz |
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+ |
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+-CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) |
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+-CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) |
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+ SED := $(filter /%,$(shell /bin/sh -c 'type sed')) |
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+ CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) |
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+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) |
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+-AR := $(filter /%,$(shell /bin/sh -c 'type ar')) |
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+ |
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+-CXXFLAGS = -O3 |
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+-CFLAGS = -O3 |
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+-LDFLAGS = |
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+ |
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+ FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog |
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+ |
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+ |
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+ |
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+ #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES |
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+-export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS |
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++export BIN_DIR SCRIPT_DIR AUX_BIN_DIR |
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+ |
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+ |
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+ |
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+@@ -114,15 +110,15 @@ |
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+ |
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+ |
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+ kurtz: |
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+- cd $(KURTZ_SRC_DIR); $(MAKE) mummer |
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++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer |
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+ |
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+ |
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+ scripts: |
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+- cd $(SCRIPT_DIR); $(MAKE) all |
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++ $(MAKE) -C $(SCRIPT_DIR) all |
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+ |
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+ |
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+ tigr: |
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+- cd $(TIGR_SRC_DIR); $(MAKE) all |
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++ $(MAKE) -C $(TIGR_SRC_DIR) all |
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+ |
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+ |
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+ uninstall: clean |
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+--- a/scripts/Makefile |
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++++ b/scripts/Makefile |
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+@@ -1,21 +1,10 @@ |
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+-#-- Imported variables from top level makefile |
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+-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS |
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++BIN_DIR = $(EPREFIX)/usr/bin |
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++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts |
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++AUX_BIN_DIR = $(EPREFIX)/usr/bin |
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+ |
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+-ifndef BIN_DIR |
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+-BIN_DIR := $(CURDIR) |
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+-endif |
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+-ifndef AUX_BIN_DIR |
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+-AUX_BIN_DIR := $(CURDIR) |
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+-endif |
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+-ifndef SCRIPT_DIR |
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+-SCRIPT_DIR := $(CURDIR) |
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+-endif |
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+- |
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+-SCRIPT_DIR := $(CURDIR) |
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+ SED := $(filter /%,$(shell /bin/sh -c 'type sed')) |
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+ CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) |
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+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) |
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+-VPATH := $(BIN_DIR) |
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+ |
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+ ALL := exact-tandems mapview mummerplot nucmer promer \ |
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+ run-mummer1 run-mummer3 nucmer2xfig dnadiff |
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+@@ -39,58 +28,49 @@ |
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+ $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ |
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+- exact-tandems.csh > $(BIN_DIR)/exact-tandems |
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+- chmod 755 $(BIN_DIR)/exact-tandems |
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++ exact-tandems.csh > exact-tandems |
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+ |
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+ mapview: mapview.pl |
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+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ |
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+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ |
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+- mapview.pl > $(BIN_DIR)/mapview |
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+- chmod 755 $(BIN_DIR)/mapview |
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++ mapview.pl > mapview |
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+ |
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+ mummerplot: mummerplot.pl Foundation.pm |
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+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ |
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+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+- mummerplot.pl > $(BIN_DIR)/mummerplot |
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+- chmod 755 $(BIN_DIR)/mummerplot |
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++ mummerplot.pl > mummerplot |
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+ |
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+ dnadiff: dnadiff.pl Foundation.pm |
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+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ |
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+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+- dnadiff.pl > $(BIN_DIR)/dnadiff |
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+- chmod 755 $(BIN_DIR)/dnadiff |
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++ dnadiff.pl > dnadiff |
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+ |
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+ nucmer: nucmer.pl Foundation.pm |
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+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ |
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+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ |
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+ -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+- nucmer.pl > $(BIN_DIR)/nucmer |
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+- chmod 755 $(BIN_DIR)/nucmer |
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++ nucmer.pl > nucmer |
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+ |
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+ promer: promer.pl Foundation.pm |
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+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ |
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+ -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ |
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+ -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+- promer.pl > $(BIN_DIR)/promer |
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+- chmod 755 $(BIN_DIR)/promer |
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++ promer.pl > promer |
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+ |
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+ run-mummer1: run-mummer1.csh |
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+ $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+- run-mummer1.csh > $(BIN_DIR)/run-mummer1 |
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+- chmod 755 $(BIN_DIR)/run-mummer1 |
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++ run-mummer1.csh > run-mummer1 |
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+ |
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+ run-mummer3: run-mummer3.csh |
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+ $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ |
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+ -e 's?__BIN_DIR?$(BIN_DIR)?g' \ |
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+- run-mummer3.csh > $(BIN_DIR)/run-mummer3 |
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+- chmod 755 $(BIN_DIR)/run-mummer3 |
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++ run-mummer3.csh > run-mummer3 |
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+ |
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+ nucmer2xfig: nucmer2xfig.pl |
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+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ |
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+- nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig |
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+- chmod 755 $(BIN_DIR)/nucmer2xfig |
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++ nucmer2xfig.pl > nucmer2xfig |
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+--- a/src/kurtz/libbasedir/Makefile |
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++++ b/src/kurtz/libbasedir/Makefile |
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+@@ -5,8 +5,6 @@ |
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+ |
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+ SPLINTFLAGS=-f ../Splintoptions -DDEBUG |
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+ |
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+-LD=$(CC) |
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+- |
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+ ##CFLAGS=${DEFINECFLAGS} |
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+ |
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+ LIBBASE=libbase.a |
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+@@ -24,14 +22,14 @@ |
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+ |
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+ |
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+ $(LIBBASE): $(LIBOBJECTS) |
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+- ar sruv $@ $(LIBOBJECTS) |
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++ $(AR) sruv $@ $(LIBOBJECTS) |
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+ |
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+ |
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+ include Filegoals.mf |
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+ |
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+ |
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+ $(LIBBASEDBG): $(LIBDEBUGOBJECTS) |
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+- ar sruv $@ $(LIBDEBUGOBJECTS) |
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++ $(AR) sruv $@ $(LIBDEBUGOBJECTS) |
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+ |
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+ |
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+ .PHONY:clean |
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+--- a/src/kurtz/Makefile |
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++++ b/src/kurtz/Makefile |
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+@@ -1,7 +1,7 @@ |
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+ all: |
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+- cd libbasedir; $(MAKE) all |
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+- cd streesrc; $(MAKE) all |
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+- cd mm3src; $(MAKE) all |
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++ $(MAKE) -C libbasedir all |
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++ $(MAKE) -C streesrc all |
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++ $(MAKE) -C mm3src all |
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+ |
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+ clean: |
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+ rm -f *~ |
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+@@ -10,11 +10,11 @@ |
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+ cd mm3src; $(MAKE) clean |
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+ |
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+ mummer: |
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+- cd libbasedir; $(MAKE) libbase.a |
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+- cd streesrc; $(MAKE) libstree.a |
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+- cd mm3src; $(MAKE) mummer |
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++ $(MAKE) -C libbasedir libbase.a |
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++ $(MAKE) -C streesrc libstree.a |
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++ $(MAKE) -C mm3src mummer |
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+ |
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+ splintall: |
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+- cd libbasedir; ${MAKE} splintall |
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+- cd streesrc; ${MAKE} splintall |
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+- cd mm3src; ${MAKE} splintall |
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++ $(MAKE) -C libbasedir splintall |
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++ $(MAKE) -C streesrc splintall |
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++ $(MAKE) -C mm3src splintall |
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+--- a/src/kurtz/mm3src/Makefile |
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++++ b/src/kurtz/mm3src/Makefile |
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+@@ -3,11 +3,7 @@ |
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+ |
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+ ##include ../Makedef |
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+ |
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+-ifndef BIN_DIR |
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+-BIN_DIR := $(CURDIR) |
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+-endif |
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+- |
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+-VPATH := $(BIN_DIR) |
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++BIN_DIR = $(EPREFIX)/usr/bin |
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+ |
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+ ALL := maxmat3.x maxmat3.dbg.x |
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+ |
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+@@ -15,11 +11,8 @@ |
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+ LIBSTREEDIR=../streesrc |
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+ INCLUDEDIR=-I${LIBBASEDIR} -I${LIBSTREEDIR} |
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+ |
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+-override CFLAGS+=$(INCLUDEDIR) |
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+-##CFLAGS=${DEFINECFLAGS} $(INCLUDEDIR) |
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+-##LDFLAGS=${DEFINELDFLAGS} |
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++override CPPFLAGS+=$(INCLUDEDIR) |
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+ SPLINTFLAGS=${INCLUDEDIR} -f ../Splintoptions -DDEBUG |
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+-LD=$(CC) |
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+ |
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+ LIBBASE=$(LIBBASEDIR)/libbase.a |
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+ LIBBASEDBG=$(LIBBASEDIR)/libbase.dbg.a |
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+@@ -40,16 +33,16 @@ |
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+ all: $(ALL) |
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+ |
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+ mummer: $(MUM3OBJECTS) $(LIBSTREE) |
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+- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ |
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+- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ |
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++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ |
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++ -o $@ |
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+ |
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+ maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE) |
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+- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ |
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+- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ |
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++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ |
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++ -o $@ |
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+ |
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+ maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG) |
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+- $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ |
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+- -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ |
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++ $(CC) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ |
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++ -lm -o $@ |
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+ |
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+ include Filegoals.mf |
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+ |
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+--- a/src/kurtz/streesrc/Makefile |
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++++ b/src/kurtz/streesrc/Makefile |
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+@@ -23,8 +23,6 @@ |
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+ |
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+ #-DSTARTFACTOR=0.5 |
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+ |
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+-LD=${CC} |
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+- |
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+ LIBBASE=${LIBBASEDIR}/libbase.a |
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+ LIBBASEDBG=${LIBBASEDIR}/libbase.dbg.a |
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+ |
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+@@ -65,29 +63,29 @@ |
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+ include Filegoals.mf |
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+ |
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+ libstree.4.a: $(OBJECTS4) |
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+- ar sruv $@ $(OBJECTS4) |
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++ $(AR) sruv $@ $(OBJECTS4) |
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+ |
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+ libstree.a: $(OBJECTS) |
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+- ar sruv $@ $(OBJECTS) |
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++ $(AR) sruv $@ $(OBJECTS) |
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+ |
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+ libstree.dbg.4.a: $(DBGOBJECTS4) |
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+- ar sruv $@ $(DBGOBJECTS4) |
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++ $(AR) sruv $@ $(DBGOBJECTS4) |
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+ |
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+ libstree.dbg.a: $(DBGOBJECTS) |
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+- ar sruv $@ $(DBGOBJECTS) |
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++ $(AR) sruv $@ $(DBGOBJECTS) |
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+ |
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+ |
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+ stree.x: stree.o libstree.a |
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+- $(LD) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@ |
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++ $(CC) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@ |
340 |
+ |
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+ loc.x: loc.o libstree.a |
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+- $(LD) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@ |
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++ $(CC) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@ |
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+ |
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+ stree.dbg.x: stree.dbg.o libstree.dbg.a |
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+- $(LD) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ |
347 |
++ $(CC) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ |
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+ |
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+ loc.dbg.x: loc.dbg.o libstree.dbg.a |
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+- $(LD) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ |
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++ $(CC) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ |
352 |
+ |
353 |
+ streeproto.h: $(PROTOFILES) Mkstreeproto.sh |
354 |
+ @echo "make $@" |
355 |
+--- a/src/tigr/Makefile |
356 |
++++ b/src/tigr/Makefile |
357 |
+@@ -1,20 +1,3 @@ |
358 |
+-#-- Imported variables from top level makefile |
359 |
+-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS |
360 |
+- |
361 |
+-ifndef BIN_DIR |
362 |
+-BIN_DIR := $(CURDIR) |
363 |
+-endif |
364 |
+-ifndef AUX_BIN_DIR |
365 |
+-AUX_BIN_DIR := $(CURDIR) |
366 |
+-endif |
367 |
+- |
368 |
+-OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@ |
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+-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ |
370 |
+- chmod 755 $(BIN_DIR)/$@ |
371 |
+-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ |
372 |
+- chmod 755 $(AUX_BIN_DIR)/$@ |
373 |
+-VPATH := $(AUX_BIN_DIR):$(BIN_DIR) |
374 |
+- |
375 |
+ ALL := annotate combineMUMs delta-filter gaps mgaps \ |
376 |
+ postnuc postpro prenuc prepro repeat-match \ |
377 |
+ show-aligns show-coords show-tiling show-snps \ |
378 |
+@@ -38,59 +21,22 @@ |
379 |
+ |
380 |
+ #-- not so PHONY rules --# |
381 |
+ delta.o: delta.cc delta.hh |
382 |
+- $(OBJ_RULE) |
383 |
+- |
384 |
+ tigrinc.o: tigrinc.cc tigrinc.hh |
385 |
+- $(OBJ_RULE) |
386 |
+- |
387 |
+ sw_align.o: sw_align.cc sw_align.hh tigrinc.hh |
388 |
+- $(OBJ_RULE) |
389 |
+- |
390 |
+ translate.o: translate.cc translate.hh |
391 |
+- $(OBJ_RULE) |
392 |
+- |
393 |
+ |
394 |
+ annotate: annotate.cc tigrinc.o |
395 |
+- $(BIN_RULE) |
396 |
+- |
397 |
+ combineMUMs: combineMUMs.cc tigrinc.o |
398 |
+- $(BIN_RULE) |
399 |
+- |
400 |
+ delta-filter: delta-filter.cc tigrinc.o delta.o |
401 |
+- $(BIN_RULE) |
402 |
+- |
403 |
+ gaps: gaps.cc tigrinc.o |
404 |
+- $(BIN_RULE) |
405 |
+- |
406 |
+ mgaps: mgaps.cc tigrinc.o |
407 |
+- $(BIN_RULE) |
408 |
+- |
409 |
+ postnuc: postnuc.cc tigrinc.o sw_align.o |
410 |
+- $(AUX_BIN_RULE) |
411 |
+- |
412 |
+ postpro: postpro.cc tigrinc.o sw_align.o translate.o |
413 |
+- $(AUX_BIN_RULE) |
414 |
+- |
415 |
+ prenuc: prenuc.cc tigrinc.o |
416 |
+- $(AUX_BIN_RULE) |
417 |
+- |
418 |
+ prepro: prepro.cc tigrinc.o translate.o |
419 |
+- $(AUX_BIN_RULE) |
420 |
+- |
421 |
+ repeat-match: repeat-match.cc tigrinc.o |
422 |
+- $(BIN_RULE) |
423 |
+- |
424 |
+ show-aligns: show-aligns.cc tigrinc.o translate.o delta.o |
425 |
+- $(BIN_RULE) |
426 |
+- |
427 |
+ show-coords: show-coords.cc tigrinc.o delta.o |
428 |
+- $(BIN_RULE) |
429 |
+- |
430 |
+ show-tiling: show-tiling.cc tigrinc.o delta.o |
431 |
+- $(BIN_RULE) |
432 |
+- |
433 |
+ show-snps: show-snps.cc tigrinc.o translate.o delta.o |
434 |
+- $(BIN_RULE) |
435 |
+- |
436 |
+ show-diff: show-diff.cc tigrinc.o delta.o |
437 |
+- $(BIN_RULE) |
438 |
|
439 |
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 |
440 |
new file mode 100644 |
441 |
index 00000000000..d6926c913d4 |
442 |
--- /dev/null |
443 |
+++ b/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch |
444 |
@@ -0,0 +1,83 @@ |
445 |
+--- a/src/kurtz/libbasedir/space.c |
446 |
++++ b/src/kurtz/libbasedir/space.c |
447 |
+@@ -379,7 +379,7 @@ |
448 |
+ } |
449 |
+ if(numberofblocks > 0) |
450 |
+ { |
451 |
+- fprintf(stderr,"space leak: number of blocks = %u\n",numberofblocks); |
452 |
++ fprintf(stderr,"space leak: number of blocks = %lu\n",numberofblocks); |
453 |
+ exit(EXIT_FAILURE); |
454 |
+ } |
455 |
+ free(blocks); |
456 |
+--- a/src/tigr/combineMUMs.cc |
457 |
++++ b/src/tigr/combineMUMs.cc |
458 |
+@@ -106,7 +106,7 @@ |
459 |
+ // This array [i] is the maximum number of errors allowed |
460 |
+ // in a match between sequences of length i , which is |
461 |
+ // i * MAXERROR_RATE . |
462 |
+-char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; |
463 |
++const char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; |
464 |
+ // Name of file to write gaps listing with # errors in each gap |
465 |
+ int Fill_Ct = 0; |
466 |
+ // Number of non-acgt bases in ref sequence |
467 |
+@@ -132,7 +132,7 @@ |
468 |
+ // The query sequence |
469 |
+ long int Query_Len; |
470 |
+ // The length of the query sequence |
471 |
+-char * Query_Suffix = "Query"; |
472 |
++const char * Query_Suffix = "Query"; |
473 |
+ // Suffix for query tag |
474 |
+ char * Ref = NULL; |
475 |
+ // The reference sequence |
476 |
+@@ -142,7 +142,7 @@ |
477 |
+ // The length of the reference sequence |
478 |
+ long int Ref_Size; |
479 |
+ // The size of the reference sequence buffer |
480 |
+-char * Ref_Suffix = "Ref"; |
481 |
++const char * Ref_Suffix = "Ref"; |
482 |
+ // Suffix for reference tag |
483 |
+ int Show_Differences = FALSE; |
484 |
+ // If TRUE then show differences in all alignments |
485 |
+--- a/src/tigr/mgaps.cc |
486 |
++++ b/src/tigr/mgaps.cc |
487 |
+@@ -64,9 +64,9 @@ |
488 |
+ static void Parse_Command_Line |
489 |
+ (int argc, char * argv []); |
490 |
+ static void Process_Matches |
491 |
+- (Match_t * A, int N, char * label); |
492 |
++ (Match_t * A, int N, const char * label); |
493 |
+ static int Process_Cluster |
494 |
+- (Match_t * A, int N, char * label); |
495 |
++ (Match_t * A, int N, const char * label); |
496 |
+ static void Union |
497 |
+ (int a, int b); |
498 |
+ static void Usage |
499 |
+@@ -438,7 +438,7 @@ |
500 |
+ |
501 |
+ |
502 |
+ static int Process_Cluster |
503 |
+- (Match_t * A, int N, char * label) |
504 |
++ (Match_t * A, int N, const char * label) |
505 |
+ |
506 |
+ // Process the cluster of matches in A [0 .. (N - 1)] and output them |
507 |
+ // after a line containing label . Return the number of clusters |
508 |
+@@ -552,7 +552,7 @@ |
509 |
+ |
510 |
+ |
511 |
+ static void Process_Matches |
512 |
+- (Match_t * A, int N, char * label) |
513 |
++ (Match_t * A, int N, const char * label) |
514 |
+ |
515 |
+ // Process matches A [1 .. N] and output them after |
516 |
+ // a line containing label . |
517 |
+--- a/src/tigr/show-coords.cc |
518 |
++++ b/src/tigr/show-coords.cc |
519 |
+@@ -788,7 +788,7 @@ |
520 |
+ (vector<AlignStats> Stats) |
521 |
+ { |
522 |
+ time_t currtime; |
523 |
+- char * type; |
524 |
++ const char * type; |
525 |
+ char date[MAX_LINE]; |
526 |
+ long int len; |
527 |
+ vector<AlignStats>::iterator Sip; |
528 |
|
529 |
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch |
530 |
new file mode 100644 |
531 |
index 00000000000..97f1dd843ac |
532 |
--- /dev/null |
533 |
+++ b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch |
534 |
@@ -0,0 +1,75 @@ |
535 |
+Use portable shebangs instead of hardcoding interpreters |
536 |
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ |
537 |
+ |
538 |
+--- a/scripts/dnadiff.pl |
539 |
++++ b/scripts/dnadiff.pl |
540 |
+@@ -1,4 +1,4 @@ |
541 |
+-#!__PERL_PATH -w |
542 |
++#!/usr/bin/env perl |
543 |
+ |
544 |
+ #------------------------------------------------------------------------------- |
545 |
+ # Programmer: Adam M Phillippy, University of Maryland |
546 |
+--- a/scripts/exact-tandems.csh |
547 |
++++ b/scripts/exact-tandems.csh |
548 |
+@@ -1,4 +1,4 @@ |
549 |
+-#!__CSH_PATH -f |
550 |
++#!/usr/bin/env csh |
551 |
+ # |
552 |
+ # Find exact tandem repeats in specified file involving an |
553 |
+ # exact duplicate of at least the specified length |
554 |
+--- a/scripts/mapview.pl |
555 |
++++ b/scripts/mapview.pl |
556 |
+@@ -1,4 +1,4 @@ |
557 |
+-#!__PERL_PATH |
558 |
++#!/usr/bin/env perl |
559 |
+ |
560 |
+ use lib "__SCRIPT_DIR"; |
561 |
+ use Foundation; |
562 |
+--- a/scripts/mummerplot.pl |
563 |
++++ b/scripts/mummerplot.pl |
564 |
+@@ -1,4 +1,4 @@ |
565 |
+-#!__PERL_PATH |
566 |
++#!/usr/bin/env perl |
567 |
+ |
568 |
+ ################################################################################ |
569 |
+ # Programmer: Adam M Phillippy, The Institute for Genomic Research |
570 |
+--- a/scripts/nucmer2xfig.pl |
571 |
++++ b/scripts/nucmer2xfig.pl |
572 |
+@@ -1,4 +1,4 @@ |
573 |
+-#!__PERL_PATH |
574 |
++#!/usr/bin/env perl |
575 |
+ # (c) Steven Salzberg 2001 |
576 |
+ # Make an xfig plot for a comparison of a reference chromosome (or single |
577 |
+ # molecule) versus a multifasta file of contigs from another genome. |
578 |
+--- a/scripts/nucmer.pl |
579 |
++++ b/scripts/nucmer.pl |
580 |
+@@ -1,4 +1,4 @@ |
581 |
+-#!__PERL_PATH |
582 |
++#!/usr/bin/env perl |
583 |
+ |
584 |
+ #------------------------------------------------------------------------------- |
585 |
+ # Programmer: Adam M Phillippy, The Institute for Genomic Research |
586 |
+--- a/scripts/promer.pl |
587 |
++++ b/scripts/promer.pl |
588 |
+@@ -1,4 +1,4 @@ |
589 |
+-#!__PERL_PATH |
590 |
++#!/usr/bin/env perl |
591 |
+ |
592 |
+ #------------------------------------------------------------------------------- |
593 |
+ # Programmer: Adam M Phillippy, The Institute for Genomic Research |
594 |
+--- a/scripts/run-mummer1.csh |
595 |
++++ b/scripts/run-mummer1.csh |
596 |
+@@ -1,4 +1,4 @@ |
597 |
+-#!__CSH_PATH -f |
598 |
++#!/usr/bin/env csh |
599 |
+ # |
600 |
+ # **SEVERELY** antiquated script for running the mummer 1 suite |
601 |
+ # -r option reverse complements the query sequence, coordinates of the reverse |
602 |
+--- a/scripts/run-mummer3.csh |
603 |
++++ b/scripts/run-mummer3.csh |
604 |
+@@ -1,4 +1,4 @@ |
605 |
+-#!__CSH_PATH -f |
606 |
++#!/usr/bin/env csh |
607 |
+ # |
608 |
+ # for running the basic mummer 3 suite, should use nucmer instead when possible |
609 |
+ # to avoid the confusing reverse coordinate system of the raw programs. |
610 |
|
611 |
diff --git a/sci-biology/mummer/mummer-3.23.ebuild b/sci-biology/mummer/mummer-3.23.ebuild |
612 |
new file mode 100644 |
613 |
index 00000000000..4839053f419 |
614 |
--- /dev/null |
615 |
+++ b/sci-biology/mummer/mummer-3.23.ebuild |
616 |
@@ -0,0 +1,46 @@ |
617 |
+# Copyright 1999-2017 Gentoo Foundation |
618 |
+# Distributed under the terms of the GNU General Public License v2 |
619 |
+ |
620 |
+EAPI=6 |
621 |
+ |
622 |
+inherit flag-o-matic toolchain-funcs |
623 |
+ |
624 |
+DESCRIPTION="A rapid whole genome aligner" |
625 |
+HOMEPAGE="http://mummer.sourceforge.net/" |
626 |
+SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz" |
627 |
+ |
628 |
+LICENSE="Artistic" |
629 |
+SLOT="0" |
630 |
+KEYWORDS="~amd64 ~x86" |
631 |
+IUSE="doc" |
632 |
+ |
633 |
+DEPEND="" |
634 |
+RDEPEND=" |
635 |
+ app-shells/tcsh |
636 |
+ dev-lang/perl" |
637 |
+ |
638 |
+S=${WORKDIR}/MUMmer${PV} |
639 |
+ |
640 |
+PATCHES=( |
641 |
+ "${FILESDIR}"/${PN}-3.23-fix-build-system.patch |
642 |
+ "${FILESDIR}"/${PN}-3.23-fix-c++-qa.patch |
643 |
+ "${FILESDIR}"/${PN}-3.23-fix-shebangs.patch |
644 |
+) |
645 |
+ |
646 |
+src_configure() { |
647 |
+ use amd64 && append-cppflags -DSIXTYFOURBITS |
648 |
+ tc-export AR CC CXX |
649 |
+} |
650 |
+ |
651 |
+src_install() { |
652 |
+ dobin src/kurtz/mm3src/mummer |
653 |
+ dobin src/tigr/{combineMUMs,delta-filter,gaps,mgaps,postnuc,postpro,prenuc,prepro,repeat-match,show-aligns,show-coords,show-tiling,show-snps,show-diff} |
654 |
+ dobin scripts/{exact-tandems,mapview,mummerplot,dnadiff,nucmer,promer,run-mummer1,run-mummer3,nucmer2xfig} |
655 |
+ newbin src/tigr/annotate mummer-annotate |
656 |
+ |
657 |
+ insinto /usr/share/${PN}/lib |
658 |
+ doins scripts/Foundation.pm |
659 |
+ |
660 |
+ einstalldocs |
661 |
+ use doc && dodoc -r docs/. |
662 |
+} |