Version bump

Package-Manager: portage-2.2_rc86/cvs/Linux x86_64

4 files changed, 138 insertions, 15 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/Manifest b/sci-biology/velvet/Manifest
index 639b206d2325..48b6c85dc186 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,19 +1,11 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX velvet-0.7.62-gentoo.diff 8934 RMD160 4fa5e7bf70c1a9adf5ad5086e856c742e72382d7 SHA1 5dccccb0f6049e0203d4008d5a00e500cf13ef74 SHA256 0c18060bc3283800d44de8895b3417782eca8fb2be4e2256c1a57f43ed628139
+AUX velvet-1.0.18-gentoo.diff 7880 RMD160 1c14bc9fa407b0cedad98e8fd4ab2b53f7906f33 SHA1 3ec1f6c2f7e16e075ab73458b16e1d5e059af983 SHA256 e67090f09c2c77bca30175c8db18dc6428556c02c4f89991ac50f7f028d9e1f0
+AUX velvet-1.0.18-gentoo.diff.bak 8012 RMD160 27d79439bb25e7c6d97f1025b823009750a61eb7 SHA1 a284b2eb52f39e3e68b18e495ed055230b4f37df SHA256 37f97e3cae4e94141d1f7ebf266a2b1a11390bd4fc98da8fc2f82a2549cbba63
 DIST velvet_0.7.55.tgz 3475289 RMD160 f27ee2f74342f09ae1da95cd011da493c3c288c1 SHA1 e4b458b70b1cf64fca09f629a95570bd09c37b0e SHA256 315331f418c2de89c6c871cea3759d947320c0adbc763fea290ec78ece69b614
 DIST velvet_0.7.62.tgz 3506366 RMD160 1e17ebc03dc135532a3eaeb6e68883116970a128 SHA1 9e5df8b4bca97d0989e06001ae93d9d5bda552b0 SHA256 fb5604dd69300fb833ad9227dce9cf38737b8d2f0a3125361eb5edebc6a4f740
+DIST velvet_1.0.18.tgz 7598196 RMD160 970e5c4222dc6a7b13a38db4c00ad300e126a516 SHA1 ce6b19d09924342c2685f8b49dcde205bb0f62a0 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e
 EBUILD velvet-0.7.55.ebuild 1720 RMD160 3fd31e44ffc0d03fbcaa4bcc347cadfb7c27f8ab SHA1 5f15b11e3954ddee5e3aff284cfd33ef84a5620a SHA256 df6d6959b07c3dab7b42756753effa4b85ca789bd6c8fd5d8a07b30700fb342b
 EBUILD velvet-0.7.62.ebuild 1504 RMD160 848be9f30b0ff82dc7b859656d54a0859e6f0690 SHA1 ddce982d92c6053bc97589dd00e0e95620e49613 SHA256 ffb3ae3c0fbd5267cf30d90b0122a1155c78e9b76543cc75d508d4d679c1f1d1
-MISC ChangeLog 1831 RMD160 e841abbbfb112277dd1ae8ea0190b2d5e48dba33 SHA1 cfd5cc2b67af5e45e9cbe71636350429ac5a6aa5 SHA256 76e03abe427a6b0f02c171da51ea3bb603b7b653583971612ec0f48b7c11c0fd
+EBUILD velvet-1.0.18.ebuild 1654 RMD160 e3bdb72d0e054936e96bc09719e01660be7235f4 SHA1 c70867f1d3a432a665a50c2d66576ed9e43554d4 SHA256 3715e3478023bf8260fc0aaa8942ded96125a360e497daed212368e5c4131b72
+MISC ChangeLog 1982 RMD160 24decea3393149e0859fbec5d6cadeeef2273bba SHA1 63f1ce1ceb483beeecbd2051ef6e312d41e8e93f SHA256 5991e03e0d1160f6f8a4e37a4cf8439ce91ad8c832bb91cc1d6bacb16b891aa1
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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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"
+}