commit: b7037b994137528a79d3e427a3a391d79ec90f38
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 10 23:48:31 2019 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Dec 10 23:48:31 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b7037b99
sci-biology/velvet: Port to EAPI 7
Package-Manager: Portage-2.3.81, Repoman-2.3.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/velvet/Manifest | 1 -
.../velvet/files/velvet-1.0.18-gentoo-r1.diff | 72 ----------------------
sci-biology/velvet/velvet-1.0.18-r1.ebuild | 53 ----------------
3 files changed, 126 deletions(-)
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 5405528bbad..e76561d597d 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,2 +1 @@
-DIST velvet_1.0.18.tgz 7598196 BLAKE2B
acaee0fef39afe34d80a6be0bcb0069fd2daab396741034fc9d298a3a828303dcba50f2cd40d94f2b97f5066b281df810716f548cd88a64ae2c661ad3e012c1f
SHA512
6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad
DIST velvet_1.2.10.tgz 18818559 BLAKE2B
5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34
SHA512
a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
deleted file mode 100644
index ed53a1229b5..00000000000
--- a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
+++ /dev/null
@@ -1,72 +0,0 @@
-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) -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 $(LIBS)
-
-
- 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) -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 $(LIBS)
-
- 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) $(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 $(LIBS)
-+ $(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 $(LIBS)
-
- 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) -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 $(LIBS)
-+ $(CC) $(CFLAGS) $(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 $(LIBS)
-
- 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) $(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 $(LIBS)
-+ $(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 $(LIBS)
-
- 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 $@
-diff -durr src/readSet.c src/readSet.c
---- src/readSet.c 2011-01-27 16:52:58.804084948 +0000
-+++ src/readSet.c 2011-01-27 17:02:55.380324786 +0000
-@@ -24,6 +24,7 @@
- #include <math.h>
- #include <time.h>
- #include <limits.h>
-+#include <zlib.h>
-
- #include "globals.h"
- #include "tightString.h"
diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild
b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
deleted file mode 100644
index a8ec87b6625..00000000000
--- a/sci-biology/velvet/velvet-1.0.18-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs flag-o-matic
-
-MY_P=${PN}_${PV}
-
-DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/";
-SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz";
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="-doc"
-KEYWORDS="amd64 x86"
-
-RDEPEND="sys-libs/zlib"
-DEPEND="${RDEPEND}
- doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
- # necessary?
- # append-flags -O3 # as recommended by upstream
- epatch "${FILESDIR}"/${P}-gentoo-r1.diff
- use doc || sed -i -e '/default :/ s/doc//' "${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/portage/make.conf, then re-emerge the
package. For example:"
- elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
-}
