Version bump

(Portage version: 2.2_rc86/cvs/Linux x86_64)

3 files changed, 133 insertions, 2 deletions

diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
index e999ee14d5a8..61b61ccedd4c 100644
--- a/sci-biology/velvet/ChangeLog
+++ b/sci-biology/velvet/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/velvet
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.12 2010/06/20 18:06:38 xarthisius Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.13 2011/02/03 02:40:47 weaver Exp $
+
+*velvet-1.0.18 (03 Feb 2011)
+
+  03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> +velvet-1.0.18.ebuild,
+  +files/velvet-1.0.18-gentoo.diff:
+  Version bump
 
   20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> -velvet-0.7.50.ebuild:
   Remove old
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo.diff
new file mode 100644
index 000000000000..b08bb3537b09
--- /dev/null
+++ b/sci-biology/velvet/files/velvet-1.0.18-gentoo.diff
@@ -0,0 +1,72 @@
+diff -durr Makefile Makefile
+--- Makefile	2011-01-27 16:52:58.853408562 +0000
++++ Makefile	2011-01-27 17:01:45.088065521 +0000
+@@ -1,8 +1,4 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
+-LDFLAGS = -lm
+-OPT = -O3
++LIBS = -lm -lz
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+@@ -41,29 +37,29 @@
+ 	-rm obj/*.o obj/dbg/*.o 
+ 
+ zlib : 
+-	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++	echo "unbundled zlib"
+ 
+ velveth : obj 
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS)  $(LDFLAGS) $(LIBS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o 
+ 
+ 
+ velvetg : obj
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS)  $(LDFLAGS) $(LIBS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o 
+ 
+ debug : override DEF := $(DEF) -D DEBUG 
+ debug : cleanobj obj/dbg
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o 
+ 
+ color : override DEF := $(DEF) -D COLOR
+ color : cleanobj obj_de
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS)  $(LDFLAGS) $(LIBS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o 
++	$(CC) $(CFLAGS)  $(LDFLAGS) $(LIBS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o 
+ 
+ colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
+ colordebug : cleanobj obj/dbg_de
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
+-	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
++	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o 
+ 
+ objdir:
+ 	mkdir -p obj
+@@ -83,7 +79,7 @@
+ obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
+ 
+ obj/%.o: src/%.c
+-	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
++	$(CC) $(CFLAGS)  $(DEF) -c $? -o $@ 
+ 
+ obj/dbg/%.o: src/%.c
+ 	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
+diff -durr src/readSet.c src/readSet.c
+--- src/readSet.c	2011-01-27 16:52:58.804084948 +0000
++++ src/readSet.c	2011-01-27 17:02:55.380324786 +0000
+@@ -24,6 +24,7 @@
+ #include <math.h>
+ #include <time.h>
+ #include <limits.h>
++#include <zlib.h>
+ 
+ #include "globals.h"
+ #include "tightString.h"
diff --git a/sci-biology/velvet/velvet-1.0.18.ebuild b/sci-biology/velvet/velvet-1.0.18.ebuild
new file mode 100644
index 000000000000..affea2dd68ce
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.0.18.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.0.18.ebuild,v 1.1 2011/02/03 02:40:47 weaver Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs flag-o-matic
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="-doc"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="doc? ( virtual/latex-base )"
+RDEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	append-flags -O3 # as recommended by upstream
+	filter-ldflags -Wl,--as-needed # sorry, no time to deal with this. patches welcome
+	epatch "${FILESDIR}"/${P}-gentoo.diff
+	use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+}
+
+src_compile() {
+	tc-export CC
+	MAKE_XOPTS=""
+	if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
+	if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
+	emake -j1 $MAKE_XOPTS || die
+	emake -j1 $MAKE_XOPTS color || die
+}
+
+src_install() {
+	dobin velvet{g,h,g_de,h_de} || die
+	insinto /usr/share/${PN}
+	doins -r contrib || die
+	dodoc Manual.pdf CREDITS.txt ChangeLog || die
+}
+
+pkg_postinst() {
+	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+	elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+	elog "	VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+}