commit: ca9bb60ca21f8e144b78bc25f119c697904d55f4 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Jan 25 14:25:36 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Jan 25 14:25:36 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca9bb60c
sci-biology/SOAPdenovo2: drop dead package does not compile, no upstream activity Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild | 40 ---- .../files/SOAPdenovo2-r241-Makefile.patch | 204 --------------------- sci-biology/SOAPdenovo2/files/soapdenovo2.1 | 22 --- sci-biology/SOAPdenovo2/metadata.xml | 12 -- 4 files changed, 278 deletions(-) diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild deleted file mode 100644 index 33fd4a2a3..000000000 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)" -HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2 - https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"; -SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" # fails to compile - -DEPEND="dev-libs/libaio - sci-biology/samtools:0.1-legacy" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241 - -src_prepare(){ - #eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch - # this will be partly covered by - # https://github.com/aquaskyline/SOAPdenovo2/pull/44 - # - for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do - sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die - done - rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \ - sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \ - standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \ - sparsePregraph/*.a || die - find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die - find -type f -name "*.h" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die - find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die - find -type f -name "*.c*" -exec sed -i -e 's/#include "bam.h"/#include "bam-0.1-legacy\/bam.h"/g' {} + || die - find -type f -name "*.c*" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die - find -type f -name "*.c*" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die - default -} diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch deleted file mode 100644 index a710c2d86..000000000 --- a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch +++ /dev/null @@ -1,204 +0,0 @@ ---- sparsePregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ sparsePregraph/Makefile 2018-04-22 22:07:47.303546845 +0200 -@@ -1,28 +1,28 @@ --CC= g++ -+CXX ?= g++ - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer -+CXXFLAGS ?= -O0 -g -fomit-frame-pointer - else --CFLAGS= -O3 -fomit-frame-pointer -w -+CXXFLAGS ?= -O3 -fomit-frame-pointer -w - endif - --DFLAGS= --OBJS= build_graph.o build_edge.o multi_threads.o \ -- build_preArc.o pregraph_sparse.o io_func.o\ -- global.o convert_soapdenovo.o --PROG= --INCLUDES= -I./inc --SUBDIRS= . --LIBPATH= -L/usr/lib64 --LIBS= -pthread -lz -L./inc -+DFLAGS = -+OBJS = build_graph.o build_edge.o multi_threads.o \ -+ build_preArc.o pregraph_sparse.o io_func.o\ -+ global.o convert_soapdenovo.o -+PROG = -+INCLUDES = -I./inc -+SUBDIRS = . -+LIBPATH = -L/usr/lib64 -+LIBS = -pthread -lz -L./inc - EXTRA_FLAGS= --VERSION = 1.0.3 -+VERSION = 1.0.3 - - ifdef 127mer --CFLAGS += -D_127MER_ -+CXXFLAGS += -D_127MER_ - PROG = pregraph_sparse_127mer.v$(VERSION) - - else --CFLAGS += -D_63MER_ -+CXXFLAGS += -D_63MER_ - PROG = pregraph_sparse_63mer.v$(VERSION) - endif - -@@ -38,22 +38,22 @@ - endif - - ifneq (,$(findstring $(shell uname -m), x86_64)) --CFLAGS += -m64 -+CXXFLAGS += -m64 - endif - - ifneq (,$(findstring $(shell uname -m), ia64)) --CFLAGS += -+CXXFLAGS += - endif - - ifneq (,$(findstring $(shell uname -m), ppc64)) --CFLAGS += -mpowerpc64 -+CXXFLAGS += -mpowerpc64 - endif - - .SUFFIXES:.cpp .o - - .cpp.o: - @printf "Compiling $<... \r" -- @$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<" -+ @$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<" - - all: $(OBJS) - @printf "$(PROG) objects generated. \n" -@@ -66,7 +66,7 @@ - - pregraph_sparse: clean envTest $(OBJS) - @printf "Linking... \r" -- @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) -+ @$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) - @printf "$(PROG) compilation done. \n" - - clean: ---- Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ Makefile 2018-04-22 22:09:16.526124921 +0200 -@@ -1,17 +1,17 @@ - MAKEFLAGS += --no-print-directory --CC = g++ -+CXX ?= g++ - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer -+CXXFLAGS ?= -O0 -g -fomit-frame-pointer - else --CFLAGS= -O3 -fomit-frame-pointer -+CXXFLAGS ?= -O3 -fomit-frame-pointer - endif - - SUBDIRS = sparsePregraph standardPregraph fusion --PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion --INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -+PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion -+INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc - --LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc --LIBS= -pthread -lz -lm -+LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc -+LIBS = -pthread -lz -lm - EXTRA_FLAGS= - - BIT_ERR = 0 -@@ -25,15 +25,15 @@ - endif - - ifneq (,$(findstring $(shell uname -m), x86_64)) --CFLAGS += -m64 -+CXXFLAGS += -m64 - endif - - ifneq (,$(findstring $(shell uname -m), ia64)) --CFLAGS += -+CXXFLAGS += - endif - - ifneq (,$(findstring $(shell uname -m), ppc64)) --CFLAGS += -mpowerpc64 -+CXXFLAGS += -mpowerpc64 - endif - - -@@ -46,20 +46,20 @@ - SOAPdenovo-63mer: - @cd sparsePregraph;make 63mer=1 debug=1;cd ..; - @cd standardPregraph;make 63mer=1 debug=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer - SOAPdenovo-127mer: - @cd sparsePregraph;make 127mer=1 debug=1;cd ..; - @cd standardPregraph;make 127mer=1 debug=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer - else - SOAPdenovo-63mer: - @cd sparsePregraph;make 63mer=1;cd ..; - @cd standardPregraph;make 63mer=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer - SOAPdenovo-127mer: - @cd sparsePregraph;make 127mer=1;cd ..; - @cd standardPregraph;make 127mer=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer - endif - - clean: ---- standardPregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ standardPregraph/Makefile 2018-04-22 22:10:33.108337752 +0200 -@@ -5,13 +5,13 @@ - # - ################################### - --CC= gcc -+CC ?= gcc - GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) - GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer #-msse4.2 -+CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2 - else --CFLAGS= -O3 -fomit-frame-pointer -w #-msse4.2 -+CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2 - endif - DFLAGS= - OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \ -@@ -24,12 +24,12 @@ - prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\ - readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \ - cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o --PROG= SOAPdenovo-63mer --INCLUDES= -Iinc --SUBDIRS= . --LIBPATH= -L/lib64 -L/usr/lib64 -L./inc --LIBS= -pthread -lz -lm --EXTRA_FLAGS= -+PROG = SOAPdenovo-63mer -+INCLUDES = -Iinc -+SUBDIRS = . -+LIBPATH = -L./inc -+LIBS = -pthread -lz -lm -+EXTRA_FLAGS = - - BIT_ERR = 0 - ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64)) ---- fusion/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ fusion/Makefile 2018-04-22 22:11:21.209727636 +0200 -@@ -6,8 +6,8 @@ - libdir = - mandir = - --CC = gcc --CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w -+CC ?= gcc -+CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w - LIBS = -lm -lpthread - INCDIRS = -Iinc/ - CFLAGS = ${CCOPT} ${INCDIRS} diff --git a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 b/sci-biology/SOAPdenovo2/files/soapdenovo2.1 deleted file mode 100644 index 337618ace..000000000 --- a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 +++ /dev/null @@ -1,22 +0,0 @@ -.TH soapdenovo2 1 "February 09, 2013" "version 2.2.3" "USER COMMANDS" -.SH NAME -soapdenovo2 \- Short-read assembly method that can build a de novo draft assembly -.SH SYNOPSIS -.B soapdenovo_63mer soapdenovo_127mer - -.SH Introduction - -SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - -1) Support large kmer up to 127 to utilize long reads. Three version are provided. - I. The 31mer version support kmer only <=31. - II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31. - III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63. - -Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version. - -For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site. - -.SH AUTHOR -Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging - diff --git a/sci-biology/SOAPdenovo2/metadata.xml b/sci-biology/SOAPdenovo2/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/SOAPdenovo2/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>
