[gentoo-commits] proj/sci:master commit in: sci-biology/zmsort/, sci-biology/zmsort/files/

[gentoo-commits] proj/sci:master commit in: sci-biology/zmsort/, sci-biology/zmsort/files/

[Justin Lecher]

commit:     f30a9287a1205e355a92a6bf273c4fd836874cfc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 15:29:27 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 15:29:27 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f30a9287

Cleaned ebuild

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/zmsort/ChangeLog                       |   10 +++++
 sci-biology/zmsort/files/zmsort-110625-build.patch |   41 ++++++++++++++++++++
 sci-biology/zmsort/zmsort-0.1.ebuild               |   40 -------------------
 sci-biology/zmsort/zmsort-110625.ebuild            |   30 ++++++++++++++
 4 files changed, 81 insertions(+), 40 deletions(-)

diff --git a/sci-biology/zmsort/ChangeLog b/sci-biology/zmsort/ChangeLog
new file mode 100644
index 0000000..7e45e0a
--- /dev/null
+++ b/sci-biology/zmsort/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/zmsort
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*zmsort-110625 (25 Jun 2011)
+
+  25 Jun 2011; Justin Lecher <jlec@gentoo.org> -zmsort-0.1.ebuild,
+  +zmsort-110625.ebuild, +files/zmsort-110625-build.patch:
+  Cleaned ebuild
+

diff --git a/sci-biology/zmsort/files/zmsort-110625-build.patch b/sci-biology/zmsort/files/zmsort-110625-build.patch
new file mode 100644
index 0000000..3c6fe8a
--- /dev/null
+++ b/sci-biology/zmsort/files/zmsort-110625-build.patch
@@ -0,0 +1,41 @@
+ Makefile |    7 +++----
+ 1 files changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 82e16a0..f9505e0 100644
+--- a/Makefile
++++ b/Makefile
+@@ -12,7 +12,7 @@ SYSTYPE :=     $(shell uname)
+ # C compiler
+ 
+ CC      := g++
+-CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE  -D_FILE_OFFSET_BITS=64 \
++CXXFLAGS  += -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE  -D_FILE_OFFSET_BITS=64 \
+  -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT
+ 
+ %.o : %.c
+@@ -25,7 +25,7 @@ CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE  -D_FILE_OFFSET_BITS=64 \
+ 	${CC} ${CFLAGS} -c $< -o $@
+ 
+ %.o : %.cpp
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.cxx
+ 	${CC} ${CFLAGS} -c $< -o $@
+@@ -33,14 +33,13 @@ CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_LARGEFILE_SOURCE  -D_FILE_OFFSET_BITS=64 \
+ # C/C++ linker
+ 
+ LINKER    := g++
+-LDFLAGS    =
+ LOADLIBES := 
+ 
+ .PHONY : all
+ all:    zmsort
+ 
+ zmsort:  ./zmsort.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
+-	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
++	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
+ 
+ # target for removing all object files
+ 

diff --git a/sci-biology/zmsort/zmsort-0.1.ebuild b/sci-biology/zmsort/zmsort-0.1.ebuild
deleted file mode 100644
index 2cec398..0000000
--- a/sci-biology/zmsort/zmsort-0.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="merge-sort utility for compressed alignment files, with multi-file output option from TIGR Gene Indices project tools"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
-		ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_prepare() {
-	# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
-	sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
-	sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
-	sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' "${S}"/"${PN}"/zmsort.cpp || die
-	cd ${PN} || die
-	ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
-}
-
-src_compile() {
-	cd ${PN} || die
-	emake || die "emake failed in "${S}"/${PN}"
-}
-
-src_install() {
-	cd ${PN} || die
-	dobin ${PN} || die "Failed to install ${PN} binary"
-	newdoc README README.${PN} || die
-}

diff --git a/sci-biology/zmsort/zmsort-110625.ebuild b/sci-biology/zmsort/zmsort-110625.ebuild
new file mode 100644
index 0000000..7d29204
--- /dev/null
+++ b/sci-biology/zmsort/zmsort-110625.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Merge-sort utility for compressed alignment files, with multi-file output"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SRC_URI="
+	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz
+	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S=${WORKDIR}/${PN}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-build.patch
+	tc-export CC CXX
+}
+
+src_install() {
+	dobin ${PN}
+	dodoc README
+}