* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mummer/, sci-biology/mummer/files/
@ 2017-03-08 22:16 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-03-08 22:16 UTC (permalink / raw
To: gentoo-commits
commit: 47a650eb48ed78b003f4449f9e7ba775a73ce9cd
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 8 21:35:39 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Mar 8 22:15:56 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=47a650eb
sci-biology/mummer: Remove old
Package-Manager: Portage-2.3.4, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4165
sci-biology/mummer/Manifest | 4 --
sci-biology/mummer/files/3.22-ldflags.patch | 16 -----
sci-biology/mummer/files/3.22-prll.patch | 56 ----------------
sci-biology/mummer/files/mummer-3.20-gcc43.patch | 12 ----
sci-biology/mummer/mummer-3.20.ebuild | 57 ----------------
sci-biology/mummer/mummer-3.21.ebuild | 52 ---------------
sci-biology/mummer/mummer-3.22-r1.ebuild | 63 ------------------
sci-biology/mummer/mummer-3.9.4_alpha.ebuild | 82 ------------------------
8 files changed, 342 deletions(-)
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
index e752ce6907b..53c34cf4516 100644
--- a/sci-biology/mummer/Manifest
+++ b/sci-biology/mummer/Manifest
@@ -1,5 +1 @@
-DIST MUMmer3.20.tar.gz 3155446 SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 SHA512 7c80bb605d57739809eb1b1cf8a579d72048e510362237d9ba64e21be18cc663769cda5dabc287832e59fb62804df34bc8336c2b42474466e7ee1e126848aecd WHIRLPOOL a08af35aee960bcd6274d3a00b1c1819d23367c81a72fd41c652c3579253b0aeeb5ef66f6dcfed60b4987c3a40830d04cd81745dce8a274cc3de0663dd54ae6f
-DIST MUMmer3.21.tar.gz 3155965 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8 SHA512 61d49e5451e1697003f7acaac690f2ede7ab71766208d3218954527c48be76ddb78d60ff40ae1bdcd4b93d3efaf21b5bd027da3722eab1ae3fa399ee726bc96e WHIRLPOOL 50c7b0d7c00bf85aa8e0f8b80bf55186f8c0a53d26c3e50d2149120bc46f3632de4cb861a4d4265c1e3be731dffb71940344b238fd3e977412134b0e401cb95e
-DIST MUMmer3.22.tar.gz 3156338 SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da SHA512 37bbb368c679d2e98fa9b9ef10c18008c173c25ee79183eb30e34125b1dc9cd10f005b7bd7c648335a8025509d8e3456fcc7ce497c95fa71c3c5d3ed3685665f WHIRLPOOL 487333ca38a9c59984ed059e8dd620ad3c0a5ae1a537e500c7b8b2d58213ac88960a13c0f25e6e0490d1209c9e73cfe8df0f8a43dbae9fd6a3e9fe3ce42da453
DIST MUMmer3.23.tar.gz 3160143 SHA256 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 WHIRLPOOL 7471d20a88f5ddf510d1e4826480706a683f005f3bab21ebb19b1fcba2c8f431435cce27a1cdf98ece8d4bb4dafcc349362037f6d526db3f564b7c013c67e882
-DIST mummer-3.9.4_alpha.tar.gz 956517 SHA256 fb2f03c729cd078d526d6318f91061f8832c2e8bd0d519ddf3c0b6e656029cfa SHA512 f0b962a69df6918afc7d163b30bcf5bd9eb2be663c8ac685b5e06317953cf12b9d240df8a5bfe8a9410b65cf88176cc7a71eecfc460e51df7ad1b27dc3a10fc2 WHIRLPOOL 8443cde87f868136eaa005db2b5b461a822097778d4c36448602a5cda058dc1dfa10daa08883248ffaba79a1d33240170b94b96548ebb56a01eaa27838d4afd6
diff --git a/sci-biology/mummer/files/3.22-ldflags.patch b/sci-biology/mummer/files/3.22-ldflags.patch
deleted file mode 100644
index d3c4a60a1ad..00000000000
--- a/sci-biology/mummer/files/3.22-ldflags.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/src/tigr/Makefile b/src/tigr/Makefile
-index cf6b9ca..5b28d1e 100644
---- a/src/tigr/Makefile
-+++ b/src/tigr/Makefile
-@@ -9,9 +9,9 @@ AUX_BIN_DIR := $(CURDIR)
- endif
-
- OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
--BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
-+BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
- chmod 755 $(BIN_DIR)/$@
--AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
-+AUX_BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
- chmod 755 $(AUX_BIN_DIR)/$@
- VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
-
diff --git a/sci-biology/mummer/files/3.22-prll.patch b/sci-biology/mummer/files/3.22-prll.patch
deleted file mode 100644
index 3b24ee40214..00000000000
--- a/sci-biology/mummer/files/3.22-prll.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 4db4977..bbd00ed 100644
---- a/Makefile
-+++ b/Makefile
-@@ -114,15 +114,15 @@ install: all
-
-
- 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
-diff --git a/src/kurtz/Makefile b/src/kurtz/Makefile
-index 85dfc16..5bff793 100644
---- 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 @@ clean:
- 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
-+ $(MAKE) -C mm3src splintall
diff --git a/sci-biology/mummer/files/mummer-3.20-gcc43.patch b/sci-biology/mummer/files/mummer-3.20-gcc43.patch
deleted file mode 100644
index 4d3edb41e46..00000000000
--- a/sci-biology/mummer/files/mummer-3.20-gcc43.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/tigr/show-diff.cc.orig 2008-06-16 17:55:34.000000000 +0000
-+++ src/tigr/show-diff.cc 2008-06-16 17:56:25.000000000 +0000
-@@ -14,6 +14,8 @@
- #include <cstdlib>
- #include <cassert>
- #include <climits>
-+#include <algorithm>
-+
- using namespace std;
-
-
-
diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild
deleted file mode 100644
index 737e6d6aa64..00000000000
--- a/sci-biology/mummer/mummer-3.20.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit eutils
-
-MY_P="MUMmer${PV}"
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
- epatch "${FILESDIR}"/${P}-gcc43.patch
- # Warning: package uses CPPFLAGS on c in addition to cpp, despite the name
- sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
- -e 's/LDFLAGS =$//' "${S}/Makefile"
-}
-
-src_compile() {
- emake || die "emake failed"
-
- sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
- -e 's|\(set bindir = \).*|\1/usr/bin|' \
- -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
- -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
- scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
- sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
-}
-
-src_install() {
- dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
- exact-tandems promer repeat-match show-aligns gaps mummer \
- show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die
- newbin annotate mummer-annotate || die
-
- insinto /usr/share/${PN}/scripts
- doins scripts/{*.awk,*.csh,*.pl}
- insinto /usr/share/${PN}/lib
- doins scripts/Foundation.pm || die
-
- dodoc ACKNOWLEDGEMENTS ChangeLog README
- insinto /usr/share/doc/${PF}
- use doc && doins -r docs
-}
diff --git a/sci-biology/mummer/mummer-3.21.ebuild b/sci-biology/mummer/mummer-3.21.ebuild
deleted file mode 100644
index e9faee09eea..00000000000
--- a/sci-biology/mummer/mummer-3.21.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit eutils
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/MUMmer${PV}"
-
-src_unpack() {
- unpack ${A}
- # Warning: package uses CPPFLAGS on c as well as cpp, despite the name
- sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
- -e 's/LDFLAGS =$//' "${S}/Makefile" || die
-}
-
-src_compile() {
- emake || die
-
- sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
- -e 's|\(set bindir = \).*|\1/usr/bin|' \
- -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
- -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
- scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
- mv annotate mummer-annotate || die
- sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
-}
-
-src_install() {
- dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
-
- insinto /usr/share/${PN}/scripts
- doins scripts/{*.awk,*.csh,*.pl} || die
- insinto /usr/share/${PN}/lib
- doins scripts/Foundation.pm || die
-
- dodoc ACKNOWLEDGEMENTS ChangeLog README
- insinto /usr/share/doc/${PF}
- use doc && doins -r docs
-}
diff --git a/sci-biology/mummer/mummer-3.22-r1.ebuild b/sci-biology/mummer/mummer-3.22-r1.ebuild
deleted file mode 100644
index f9caede7641..00000000000
--- a/sci-biology/mummer/mummer-3.22-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="3"
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/MUMmer${PV}"
-
-src_prepare() {
- use amd64 && append-flags -DSIXTYFOURBITS
-
- epatch \
- "${FILESDIR}"/${PV}-prll.patch \
- "${FILESDIR}"/${PV}-ldflags.patch
-
- sed \
- -e '/^CFLAGS/d' \
- -e '/^CXXFLAGS/d' \
- -e '/^LDFLAGS/d' \
- -i Makefile || die
-}
-
-src_compile() {
- emake || die
-
- sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
- -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
- -e 's|\(set bindir = \).*|\1/usr/bin|' \
- -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
- -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
- scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
- mv annotate mummer-annotate || die
- sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
-}
-
-src_install() {
- dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
-
- insinto /usr/share/${PN}/scripts
- doins scripts/{*.awk,*.csh,*.pl} || die
- insinto /usr/share/${PN}/lib
- doins scripts/Foundation.pm || die
-
- dodoc ACKNOWLEDGEMENTS ChangeLog README || die
- insinto /usr/share/doc/${PF}
- if use doc; then
- doins -r docs || die
- fi
-}
diff --git a/sci-biology/mummer/mummer-3.9.4_alpha.ebuild b/sci-biology/mummer/mummer-3.9.4_alpha.ebuild
deleted file mode 100644
index 2865c3d9b2e..00000000000
--- a/sci-biology/mummer/mummer-3.9.4_alpha.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit perl-functions python-r1 toolchain-funcs
-
-MY_PV=${PV//_/}
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="https://github.com/gmarcais/${PN}/releases/download/v${MY_PV}/${PN}-${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="openmp perl python"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- python? (
- ${PYTHON_DEPS}
- dev-lang/swig:0
- )"
-RDEPEND="
- app-shells/tcsh
- dev-lang/perl:=
- python? ( ${PYTHON_DEPS} )"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S=${WORKDIR}/${PN}-${MY_PV}
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
- use python && preamble="python_foreach_impl run_in_build_dir"
-}
-
-src_configure() {
- perl_set_version
- configure() {
- local pythonconf
- if use python; then
- pythonconf="--enable-python-binding=$(python_get_sitedir)"
- else
- pythonconf="--disable-python-binding"
- fi
-
- ECONF_SOURCE="${S}" econf \
- --disable-static \
- --disable-ruby-binding \
- $(use_enable perl perl-binding "${VENDOR_LIB}") \
- $(use_enable openmp) \
- $(use_enable python swig) \
- "${pythonconf}"
- }
- ${preamble} configure
-}
-
-src_compile() {
- ${preamble} default
-}
-
-src_install() {
- ${preamble} default
- einstalldocs
-
- # avoid file collision
- mv "${ED%/}"/usr/bin/{,mummer-}annotate || die
-
- # move perl module into right place
- mkdir -p "${D%/}${VENDOR_LIB}" || die
- mv "${ED%/}"/usr/$(get_libdir)/mummer/Foundation.pm "${D%/}${VENDOR_LIB}" || die
-
- # no static libs, can purge .la files
- find "${D}" -name '*.la' -delete || die
-}
^ permalink raw reply related [flat|nested] 2+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/mummer/, sci-biology/mummer/files/
@ 2017-03-08 22:16 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-03-08 22:16 UTC (permalink / raw
To: gentoo-commits
commit: 11d10cd16517dbbba9573653b1909995a4033571
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 8 21:35:39 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Mar 8 22:15:49 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=11d10cd1
sci-biology/mummer: Version bump to 3.23
* EAPI 6
* Make build system saner
* Fix C++ QA warnings
Package-Manager: Portage-2.3.4, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4165
sci-biology/mummer/Manifest | 1 +
.../files/mummer-3.23-fix-build-system.patch | 397 +++++++++++++++++++++
.../mummer/files/mummer-3.23-fix-c++-qa.patch | 83 +++++
.../mummer/files/mummer-3.23-fix-shebangs.patch | 75 ++++
sci-biology/mummer/mummer-3.23.ebuild | 46 +++
5 files changed, 602 insertions(+)
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
index 8089124a742..e752ce6907b 100644
--- a/sci-biology/mummer/Manifest
+++ b/sci-biology/mummer/Manifest
@@ -1,4 +1,5 @@
DIST MUMmer3.20.tar.gz 3155446 SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 SHA512 7c80bb605d57739809eb1b1cf8a579d72048e510362237d9ba64e21be18cc663769cda5dabc287832e59fb62804df34bc8336c2b42474466e7ee1e126848aecd WHIRLPOOL a08af35aee960bcd6274d3a00b1c1819d23367c81a72fd41c652c3579253b0aeeb5ef66f6dcfed60b4987c3a40830d04cd81745dce8a274cc3de0663dd54ae6f
DIST MUMmer3.21.tar.gz 3155965 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8 SHA512 61d49e5451e1697003f7acaac690f2ede7ab71766208d3218954527c48be76ddb78d60ff40ae1bdcd4b93d3efaf21b5bd027da3722eab1ae3fa399ee726bc96e WHIRLPOOL 50c7b0d7c00bf85aa8e0f8b80bf55186f8c0a53d26c3e50d2149120bc46f3632de4cb861a4d4265c1e3be731dffb71940344b238fd3e977412134b0e401cb95e
DIST MUMmer3.22.tar.gz 3156338 SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da SHA512 37bbb368c679d2e98fa9b9ef10c18008c173c25ee79183eb30e34125b1dc9cd10f005b7bd7c648335a8025509d8e3456fcc7ce497c95fa71c3c5d3ed3685665f WHIRLPOOL 487333ca38a9c59984ed059e8dd620ad3c0a5ae1a537e500c7b8b2d58213ac88960a13c0f25e6e0490d1209c9e73cfe8df0f8a43dbae9fd6a3e9fe3ce42da453
+DIST MUMmer3.23.tar.gz 3160143 SHA256 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 WHIRLPOOL 7471d20a88f5ddf510d1e4826480706a683f005f3bab21ebb19b1fcba2c8f431435cce27a1cdf98ece8d4bb4dafcc349362037f6d526db3f564b7c013c67e882
DIST mummer-3.9.4_alpha.tar.gz 956517 SHA256 fb2f03c729cd078d526d6318f91061f8832c2e8bd0d519ddf3c0b6e656029cfa SHA512 f0b962a69df6918afc7d163b30bcf5bd9eb2be663c8ac685b5e06317953cf12b9d240df8a5bfe8a9410b65cf88176cc7a71eecfc460e51df7ad1b27dc3a10fc2 WHIRLPOOL 8443cde87f868136eaa005db2b5b461a822097778d4c36448602a5cda058dc1dfa10daa08883248ffaba79a1d33240170b94b96548ebb56a01eaa27838d4afd6
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 00000000000..b92f75c0771
--- /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 00000000000..d6926c913d4
--- /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 00000000000..97f1dd843ac
--- /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/mummer-3.23.ebuild b/sci-biology/mummer/mummer-3.23.ebuild
new file mode 100644
index 00000000000..4839053f419
--- /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/.
+}
^ permalink raw reply related [flat|nested] 2+ messages in thread
end of thread, other threads:[~2017-03-08 22:17 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2017-03-08 22:16 [gentoo-commits] repo/gentoo:master commit in: sci-biology/mummer/, sci-biology/mummer/files/ David Seifert
-- strict thread matches above, loose matches on Subject: below --
2017-03-08 22:16 David Seifert
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox