From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/consed/Manifest | 10 + sci-biology/consed/consed-29.ebuild | 110 ++++ .../consed/files/consed-29-fix-build-system.patch | 197 ++++++ sci-biology/consed/files/consed-29-fix-c++14.patch | 376 +++++++++++ .../consed/files/consed-29-fix-perl-shebang.patch | 701 +++++++++++++++++++++ sci-biology/consed/files/consed-29-fix-qa.patch | 275 ++++++++ sci-biology/consed/metadata.xml | 8 + 7 files changed, 1677 insertions(+) create mode 100644 sci-biology/consed/Manifest create mode 100644 sci-biology/consed/consed-29.ebuild create mode 100644 sci-biology/consed/files/consed-29-fix-build-system.patch create mode 100644 sci-biology/consed/files/consed-29-fix-c++14.patch create mode 100644 sci-biology/consed/files/consed-29-fix-perl-shebang.patch create mode 100644 sci-biology/consed/files/consed-29-fix-qa.patch create mode 100644 sci-biology/consed/metadata.xml (limited to 'sci-biology/consed') diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest new file mode 100644 index 000000000000..e997d2a6f419 --- /dev/null +++ b/sci-biology/consed/Manifest @@ -0,0 +1,10 @@ +AUX consed-29-fix-build-system.patch 5614 SHA256 652a970de74eebf12e7b7693bbbc953d4bb6662c29ab970d39c8b696ad0b2cfc SHA512 ea649079d5dbff21206bf8f56729fc559f374120dd3336499677eb65fde247739f41efdb29a3df60225ec38efc6802608aa2410bf4ab77f8d76bfd31fdc710fa WHIRLPOOL 597ee496f0a85371e9324d05c71350227945f6d436732347f4e86a2ccccdc59d948c41646bb78215275baa677d9e377dc88146267fd8d6cc01f4b32de4177482 +AUX consed-29-fix-c++14.patch 9261 SHA256 1cbd45895b083c3e8ff553f56da0e19d8e67866df8e38026e40252e20f8ab109 SHA512 be5cd76d36cf437c1113d09e540d98d0eb92b7e2e732f4a5a308066b8046b5628048203e791a0fa316e44a4cc127d027418a7f038406df22c3f60552f5b87789 WHIRLPOOL eddfeb0f11561107ff174adf0acfb3b6440f803b2b7410d372748fd1c2dad04185ca25e59c99a4d9c137af69f2f00be1bf9bf6a5813c5ca07a5afff6cee382f6 +AUX consed-29-fix-perl-shebang.patch 17375 SHA256 cdf3d2868fc69c2ff62897031d7e57e4b215b9d33ef07411fafd193fec2ea380 SHA512 4caed1ab7229e2b3e367f03a8d650cafed2974232fcd6daa08e62c90512d49e09caceb34c5bb65c67a588bab314165d72d8c1687393549d4107425df78e3218d WHIRLPOOL 7f7c36100a995f733bb126e637f470e4191cfd0dfb066ccce2fce6e7cd46cdc217811aed969c9235f5a9d64ecc032f6f3366a2744665c94ac486b714619cc6d7 +AUX consed-29-fix-qa.patch 11168 SHA256 8d024a5a8ac13411dfbe621ea7e9a968a802f2169822fb917085408e0d1eee44 SHA512 088d774159b421666bf75f6f9f17ee83d488625d482d8d404bde12671025b1f03322bee5c50e792fbbd822c223fa5ee697cf99c7efc9fcbebc119314d02df604 WHIRLPOOL d5464e848ad6af177963908eda8f18e7999faaaba50e67b05a9b7f365e24c6e6e49146afc922801b0f6ce7e6dbd372c2dc7c9709b3047aa3b2ded9f2e93cb9d6 +DIST consed-29-linux.tar.gz 36172715 SHA256 98354e2507ef9026b82c89db199ff1de7e4ec3686fccd691d215acdcde34ce39 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd WHIRLPOOL 26ebc1ee7114b0c609fd36c2c46b71c399bacb61f7db285ab36f296902964c14518c058e814a166b20a36c2d320280aeed0ca18b7104c6b503324bf27d4b57af +DIST consed-29-sources.tar.gz 3258845 SHA256 e7d3c2bf60e0bb22025e0416d16cf9864fec8091811ec285a39db4cb46bc3fc6 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 WHIRLPOOL 5ac363f049b6b40554112f830e812e7ab7d334a0f6707ea4da981ed1e468109f3bd7669382aa77e93cf12c78cc95fb1085711dcc972c7ff22ffe6b73056bb2c2 +EBUILD consed-29.ebuild 2701 SHA256 7470245178f4f819cc0f150a93bd69600be1419d1cc03568f4c8df812f03cffb SHA512 56d73a2d4ed207924c2a7676bfca84b8c0cc4f80d1a2a1b94fa2b3d644a6583f15e32ee81b9892122e051f17a1eda56d63ffb8d650283a9bee5c61bca6faf1d3 WHIRLPOOL 4ada9787bb4aee8fedff7c2d5f8fbf1797fb0f9a4b0d0e8c28a44c001b5c2cf2e95e2025342a1a63e0c63af0fc586b0dddd62ebe6c8b85d4e0a32dac1f31b92c +MISC ChangeLog 3099 SHA256 32a35743568e4401c24020f6c7987a1232d330d471a6ecbc94a914c88f899c4d SHA512 aee79f35f12c66eea2b4b2f8c263378a9677f4b38a73b80a2b6d52fe8506e7ca5378d20dc76bcce161928eda1a28473d73ec5d2e6fb124ad57fc5dcd534185a3 WHIRLPOOL c00113b1e85009fa1617952f210ebdb5355da651be99e980154430eb277436592c6fe89707f6a3c340c8ab5f63a3082301eeb6345500bdb38b1a2029575b8951 +MISC ChangeLog-2015 1550 SHA256 e110efe81735bbf632bf4a714561ab23dd49b8c03e0e34e0d062041e95ccd3f5 SHA512 f75dcb91ca84cdc363871da94fdb50369bc213f76e3d0e97ee2efbe352721e7994ffe53e92e96f326af5a552eb8edd1d895f839939be7e27f91e5cc5d230ae14 WHIRLPOOL a09fa21234435824b67947e0db03020e18fc6621ca9303478200849f5fe503369c7efb8fcfffcceec89998b971e49cb40ec92db40d6515fbc174eb3c45822c9f +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild new file mode 100644 index 000000000000..d5417e310281 --- /dev/null +++ b/sci-biology/consed/consed-29.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="A genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI=" + ${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +COMMON_DEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + sci-biology/samtools:0.1-legacy +" +DEPEND=" + ${COMMON_DEPEND} + virtual/pkgconfig +" +RDEPEND=" + ${COMMON_DEPEND} + dev-lang/perl + >=sci-biology/phred-071220-r1 + >=sci-biology/phrap-1.080812-r2 +" + +S="${WORKDIR}" + +RESTRICT="fetch" +PATCHES=( + "${FILESDIR}/${PN}-29-fix-build-system.patch" + "${FILESDIR}/${PN}-29-fix-c++14.patch" + "${FILESDIR}/${PN}-29-fix-qa.patch" + "${FILESDIR}/${PN}-29-fix-perl-shebang.patch" +) + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + default + + sed \ + -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ + -e "s:/usr/local/genome:${EPREFIX}/usr:" \ + -e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \ + -e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \ + -i scripts/* contributions/* || die +} + +src_configure() { + append-cflags -std=gnu99 + append-lfs-flags +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \ + LIBS="-L${EPREFIX}/usr/$(get_libdir)" \ + X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \ + SAMTOOLS_LIBS="-lbam-0.1-legacy" +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/* + + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} + + if use examples; then + insinto /usr/share/${PN}/examples + doins -r \ + standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer + fi + + cat > 99consed <<-_EOF_ || die + CONSED_HOME=${EPREFIX}/usr + CONSED_PARAMETERS=${EPREFIX}/etc/consedrc + _EOF_ + doenvd 99consed + + dodoc README.txt *_announcement.txt +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch new file mode 100644 index 000000000000..27c9c552fe3f --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-build-system.patch @@ -0,0 +1,197 @@ +Make build system semi-sane: +* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS +* Remove default optimisation flags +* Remove -fpermissive from DEFS (as source builds fine now) +* Add large file support (LFS) via CPPFLAGS and not in Makefile + +--- a/makefile ++++ b/makefile +@@ -47,23 +47,20 @@ + # + # compilation + # +-CXX= g++ +-KRCC= gcc +-CC=gcc ++CXX ?= g++ ++CC ?= gcc + + # + # +-CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE ++DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE + +-OPT= -O + # + # Include directory for template classes must be included + # in both compilation & link lines, even if .h file is + # found in default path. C front, gotta love it. + # +-INC= -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18 ++INCLUDES = $(SAMTOOLS_CPPFLAGS) + +-DEPENDENCIES= + # + # + # Linking +@@ -80,12 +77,9 @@ + # /lib/ld-linux.so.2 (0x003ee000) + # + # To fix cut/paste bug, I've made X11 always dynamic. +-CLIBS= -lX11 +-LPATH= -L/usr/X11R6/lib +-ARCHIVES= /usr/X11R6/lib/libXm.a \ +-/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \ +-/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \ +-/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a ++ ++MOTIF_LIBS ?= -lXt -lXm ++ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS) + + + +@@ -94,7 +88,6 @@ + # + #LDFLGS= -g + # static linking +-LDFLGS= -g -rdynamic + + # + # the subdirectory used by cfront compilers gets cleaned +@@ -112,10 +105,10 @@ + # general compilation rules for .cpp, .cxx, .c files + # + .cpp.o: +- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< + + .c.o: +- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< + + # + # targets file included in generated makefile +@@ -593,17 +586,23 @@ + writeToRewriteReferenceFile.o \ + xsynchronize.o + ++SUBDIRS := misc/454 misc/mktrace misc/phd2fasta ++ ++all: consed $(SUBDIRS) ++ ++$(SUBDIRS): ++ $(MAKE) -C $@ ++ ++.PHONY: all $(SUBDIRS) ++ + consed: $(CONSED_OBJS) makefile checkLicenseKeyStub.o +- $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ +- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) + + trial_consed: $(CONSED_OBJS) makefile checkLicenseKey.o +- $(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \ +- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS) + + pure: $(CONSED_OBJS) makefile checkLicenseKeyStub.o +- $(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ +- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) + + clean: + rm -rf *.o core $(TEMPLATE_DIR) +@@ -613,15 +612,15 @@ + # the Solaris 5.x compiler cannot optimize the following + + consedResources.o: +- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp + + consedResources2.o: +- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp + + # tlingit cannot optimize the following: + + guiEditResources.o: +- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp + + guiEditResources.o : \ + assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \ +--- a/misc/454/Makefile ++++ b/misc/454/Makefile +@@ -0,0 +1,16 @@ ++CC ?= cc ++LIBM = -lm ++ ++DEFS = -DANSI_C ++ ++OBJS= sff2scf.c ++ ++sff2scf: $(OBJS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) ++ ++.c.o: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< ++ ++clean: ++ rm -f $(OBJS) sff2scf ++ +--- a/misc/mktrace/Makefile ++++ b/misc/mktrace/Makefile +@@ -1,13 +1,17 @@ +-CC= cc +-CFLAGS= -g +-CLIB= -lm ++CC ?= cc ++LIBM = -lm ++ ++DEFS = -DANSI_C + + OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \ + freeTrace.o rwUtil.o writePhd.o getTime.o \ + readQUAL.o + + mktrace: $(OBJS) +- $(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) ++ ++.c.o: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< + + clean: + rm -f $(OBJS) mktrace +--- a/misc/phd2fasta/Makefile ++++ b/misc/phd2fasta/Makefile +@@ -1,8 +1,9 @@ +-CC=cc +-CFLAGS=-O -w +-CLIB=-lm ++CC ?= cc ++LIBM = -lm + +-OBJ= phd2fasta.o \ ++DEFS = -DANSI_C ++ ++OBJS= phd2fasta.o \ + readParam.o initParam.o checkParam.o \ + freeParam.o helpParam.o \ + readFOF.o readDIR.o readFOX.o \ +@@ -15,10 +16,11 @@ + + INC= phd2fasta.h + +-SRC = $(OBJ:.o=.c) +- +-phd2fasta: $(OBJ) +- $(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB) ++phd2fasta: $(OBJS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) ++ ++.c.o: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< + + clean: + rm -f $(OBJ) phd2fasta diff --git a/sci-biology/consed/files/consed-29-fix-c++14.patch b/sci-biology/consed/files/consed-29-fix-c++14.patch new file mode 100644 index 000000000000..212b8d63d1e3 --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-c++14.patch @@ -0,0 +1,376 @@ +Fix building with C++14: +* Add 'noexcept(false)' to throwing destructors in C++11 mode +* Properly guard C declarations with extern "C" scopes +* Avoid erroneous overloaded suffix operator errors, due to missing spaces +* Add explicit casts to avoid -Wnarrowing errors +* Add 'this->' for dependent identifiers in derived class templates, + previously required -fpermissive + +--- a/bvAlignedReads.cpp ++++ b/bvAlignedReads.cpp +@@ -126,7 +126,11 @@ + } + + +-bvAlignedReads :: ~bvAlignedReads() { ++bvAlignedReads :: ~bvAlignedReads() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++{ + + + assert( pBamView_->aBVAlignedReads_.remove( this ) ); +--- a/bvAlignedReads.h ++++ b/bvAlignedReads.h +@@ -81,7 +81,11 @@ + const FileName& filReferenceSequenceFile, + bamView* pBamView ); + +- ~bvAlignedReads(); ++ ~bvAlignedReads() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + bool operator==( const bvAlignedReads& myBVAlignedReads ) const { + return( this == &myBVAlignedReads ); +--- a/chromatData.h ++++ b/chromatData.h +@@ -58,6 +58,9 @@ + #ifndef CHROMATDATA_DEFINED + #define CHROMATDATA_DEFINED + ++#ifdef __cplusplus ++extern "C" { ++#endif + + #ifndef FLOAT + #define FLOAT double +@@ -131,4 +134,8 @@ + int freeChromatData(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/compareContigs.cpp ++++ b/compareContigs.cpp +@@ -126,6 +126,9 @@ + + + compareContigs :: ~compareContigs() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + + if ( !bCalledFromMakeJoins_ ) { +--- a/compareContigs.h ++++ b/compareContigs.h +@@ -137,7 +137,11 @@ + compareContigs( ContigWin* pContigWin, const int nConsPos1); + compareContigs(); // for assemblyView + +- ~compareContigs(); ++ ~compareContigs() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + // this makes RWTPtrOrderedVector in ConsEd happy + bool operator==( const compareContigs& compC ) const { + +--- a/filePopupAndGetAceFilename.cpp ++++ b/filePopupAndGetAceFilename.cpp +@@ -317,7 +317,7 @@ + struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); + + strftime( szDateTime, nDateTimeSize, +- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", ++ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", + pTM ); + + RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); +@@ -620,7 +620,7 @@ + struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); + + strftime( szDateTime, nDateTimeSize, +- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", ++ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", + pTM ); + + RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); +--- a/findTraceExtrema.h ++++ b/findTraceExtrema.h +@@ -44,8 +44,15 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + int findTraceExtrema( ChromatData *chromatData ); + ++#ifdef __cplusplus ++} ++#endif + + #endif + +--- a/makeUpper.h ++++ b/makeUpper.h +@@ -42,6 +42,14 @@ + #ifndef MAKEUPPER_INCLUDED + #define MAKEUPPER_INCLUDED + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + void makeUpper( char* szStringOfMixedCase ); + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/nextPhredPipeline.cpp ++++ b/nextPhredPipeline.cpp +@@ -476,7 +476,7 @@ + void nextPhredPipeline :: openAndLockControlFile() { + + +- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR ); ++ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600); + if ( nFDControlFile_ == -1 ) { + THROW_FILE_ERROR( filControlFile_ ); + } +--- a/readABI.h ++++ b/readABI.h +@@ -56,10 +56,18 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + #ifdef ANSI_C + ChromatData *readABI( char *fn, int *status ); + #else + ChromatData *readABI(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/readData.h ++++ b/readData.h +@@ -44,6 +44,14 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + ChromatData *readData( char *filename, int* status ); + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/readESD.h ++++ b/readESD.h +@@ -53,6 +53,10 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + typedef unsigned int4 DWORD; + typedef unsigned char TCHAR; + typedef char BYTE; +@@ -187,5 +191,7 @@ + ChromatData *readESD(); + #endif + +- ++#ifdef __cplusplus ++} ++#endif + +--- a/readSCF.h ++++ b/readSCF.h +@@ -56,6 +56,10 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + /* ---- Constants ---- */ + #define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f') + #define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX ) +@@ -144,4 +148,8 @@ + int readSCF3(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/readsense_bitmaps.h ++++ b/readsense_bitmaps.h +@@ -56,10 +56,10 @@ + static const int forward_bitmap_height = 19; + static char forward_bitmap_bits[] = { + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, +- 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, +- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0xff, 0x3f, 0x00, 0xf8, 0xff, 0xff, 0x07, +- 0xf8, 0xff, 0xff, 0x0f, 0xf8, 0xff, 0xff, 0x07, 0xf8, 0xff, 0x1f, 0x00, +- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, ++ 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, ++ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, (char)0xff, 0x3f, 0x00, (char)0xf8, (char)0xff, (char)0xff, 0x07, ++ (char)0xf8, (char)0xff, (char)0xff, 0x0f, (char)0xf8, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, 0x1f, 0x00, ++ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, + 0x00, 0x00, 0x00, 0x00}; + +@@ -67,10 +67,10 @@ + static const int reverse_bitmap_height = 19; + static char reverse_bitmap_bits[] = { + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, +- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, 0xf8, 0x07, +- 0x00, 0xc0, 0xff, 0x07, 0x00, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, +- 0xfc, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, 0x00, 0xfe, 0xff, 0x07, +- 0x00, 0xc0, 0xff, 0x07, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, ++ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, (char)0xf8, 0x07, ++ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, ++ (char)0xfc, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, 0x00, (char)0xfe, (char)0xff, 0x07, ++ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, + 0x00, 0x00, 0x00, 0x00}; + +--- a/readType.h ++++ b/readType.h +@@ -56,11 +56,19 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + #ifdef ANSI_C + int readType( char *filename ); + #else + int readType(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif + +--- a/rwtptrsortedvector.h ++++ b/rwtptrsortedvector.h +@@ -57,7 +57,6 @@ + #ifdef USE_USING_IN_PUBLIC_TEMPLATE_CLASSES + using RWTPtrOrderedVector::nCurrentLength_; + using RWTPtrOrderedVector::isEmpty; +- using RWTPtrOrderedVector::nCurrentLength_; + using RWTPtrOrderedVector::length; + using RWTPtrOrderedVector::ppArray_; + using RWTPtrOrderedVector::data; +@@ -84,7 +83,7 @@ + if ( nInsertBeforeIndex == RW_NPOS ) + nInsertBeforeIndex = nCurrentLength_; + +- insertAt( nInsertBeforeIndex, pVal ); ++ this->insertAt( nInsertBeforeIndex, pVal ); + } + + // don't copy this. copy mbtValOrderedVectorOfRWCString's method instead +--- a/rwtvalsortedvector.h ++++ b/rwtvalsortedvector.h +@@ -74,7 +74,7 @@ + if ( nPos == RW_NPOS ) + nPos = nCurrentLength_; + +- insertAt( nPos, val ); ++ this->insertAt( nPos, val ); + } + + +--- a/rwUtil.h ++++ b/rwUtil.h +@@ -51,6 +51,10 @@ + *|***************************************************************************|* + */ + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + #ifdef ANSI_C + int2 inSwpSint2( char *ptr ); + int4 inSwpSint4( char *ptr ); +@@ -97,3 +101,6 @@ + int writeUint4(); + #endif + ++#ifdef __cplusplus ++} ++#endif +--- a/soGetDateTime.cpp ++++ b/soGetDateTime.cpp +@@ -62,13 +62,13 @@ + else if ( nFormat == nDotInMiddle ) { + strftime( szDateTime, + nDateTimeSize, +- "%y%m%d."quote(%H)quote(%M)quote(%S), ++ "%y%m%d." quote(%H)quote(%M)quote(%S), + localtime( &timee ) ); + } + else { + strftime( szDateTime, + nDateTimeSize, +- "%y%m%d:"quote(%H)quote(%M)quote(%S), ++ "%y%m%d:" quote(%H)quote(%M)quote(%S), + localtime( &timee ) ); + } + +--- a/szGetTime.h ++++ b/szGetTime.h +@@ -42,9 +42,15 @@ + #ifndef szGetTime_included + #define szGetTime_included + +-char *szGetTime(); ++#ifdef __cplusplus ++extern "C" { ++#endif + ++char *szGetTime(); + ++#ifdef __cplusplus ++} ++#endif + + #endif + diff --git a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch new file mode 100644 index 000000000000..a27a3537a8d1 --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch @@ -0,0 +1,701 @@ +Make perl shebangs portable, such that the scripts can also be used on Gentoo Prefix. +Rationale: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/contributions/ace2fof ++++ b/contributions/ace2fof +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # .-----------------------------------------------------------------------------------. + # | | +@@ -107,6 +107,7 @@ + # | | + # `-----------------------------------------------------------------------------------' + #Fixed this file for taking Aracne's Ace file by syang 05152002 ++use warnings; + use strict; + use POSIX qw(fmod); + +--- a/contributions/ace2OligosWithComments.perl ++++ b/contributions/ace2OligosWithComments.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # ace2Oligos.perl + # +@@ -18,6 +18,8 @@ + # Rev: 020528 to print comments in oligo tags upon request (Peter Kos) + # + ++use warnings; ++ + $szUsage = "\nUsage: $0 (name of ace file) (name of oligo file) [Print|Comment|PrintComment]\n"; + + die "$szUsage" if (( $#ARGV != 1 ) && ( $#ARGV != 2 )); +--- a/contributions/aceContigs2Phds.perl ++++ b/contributions/aceContigs2Phds.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # aceContigs2Phd.perl + # +@@ -13,6 +13,8 @@ + # Acknowledgements: Borrowed as much as I could from determineReadTypes.Perl + # and fasta2Phd.perl + ++use warnings; ++ + $szUsage = "Usage: aceContigs2Phds.perl [-s minimum-contig-size] "; + $nContigLimit = 2000; + +--- a/contributions/acestatus.pl ++++ b/contributions/acestatus.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # acestatus.pl + # author: Cliff Wollam +@@ -14,6 +14,7 @@ + # USAGE FROM THE COMMAND LINE: + # acestatus.pl ace_filename + ++use warnings; + use strict; + + if($#ARGV >= 0) { +--- a/contributions/cons.perl ++++ b/contributions/cons.perl +@@ -1,5 +1,6 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + ++use warnings; + use strict; + use Cwd; + +--- a/contributions/mergeAces.perl ++++ b/contributions/mergeAces.perl +@@ -1,4 +1,4 @@ +-#! /usr/local/bin/perl -w ++#!/usr/bin/env perl + + # Bugs and complaints to Bill Gilliland, billg@ucdavis.edu. + # mergeAces.perl v. 0.2 5/22/01 +@@ -9,6 +9,7 @@ + # project directory (if it doesn't already exist) with all the cgrams + # and phd files of the original projects. + ++use warnings; + use Getopt::Long; + use File::Copy; + $pathRoot = $ENV{"PWD"}; +--- a/contributions/phredPhrapWithPhdBalls ++++ b/contributions/phredPhrapWithPhdBalls +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # phredPhrapWithPhdBalls + # modified from phredPhrap by Ben Allen at LANL +@@ -73,6 +73,7 @@ + # Rev: 120312 to not duplicate consensus tags during miniassembly + # Rev: 120717 Ben Allen (LANL) to use reads from phdballs as well as phd_dir + ++use warnings; + + $szVersion = "120312"; + +--- a/contributions/recover_consensus_tags ++++ b/contributions/recover_consensus_tags +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # Purpose: Transfers all consensus tags from a set of old assemblies to + # a new assembly. +@@ -14,6 +14,7 @@ + # rct ace_filename + # You must be in the edit_dir where the ace file is located + ++use warnings; + use strict; + + +--- a/contributions/revert_fof ++++ b/contributions/revert_fof +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: If the user really screws up a read, to back out all changes. + # You must reassemble after using this. +@@ -19,6 +19,8 @@ + # phd extensions. + # revert_fof use file of files to give reads to revert 3/14/01 SL + ++use warnings; ++ + $szUsage = "Enter a file of files name, please!"; + + die $szUsage if ( $#ARGV != 0 ); +--- a/contributions/sff2phd.perl ++++ b/contributions/sff2phd.perl +@@ -1,4 +1,5 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++use warnings; + use strict; + # SFF to PHD files converter, with 454 paired reads and MID support + # Version 0.15 - 111229 +--- a/contributions/sff2phd_Samborskyy ++++ b/contributions/sff2phd_Samborskyy +@@ -1,4 +1,5 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++use warnings; + use strict; + # SFF to PHD files converter, with 454 paired reads and MID support + # Version 0.10 - 101110 +--- a/scripts/ace2Fasta.perl ++++ b/scripts/ace2Fasta.perl +@@ -1,7 +1,9 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Purpose: makes a contigs file out of an ace file + ++use warnings; ++ + $szUsage = "Usage: ace2Contigs.perl (ace file)"; + + +--- a/scripts/ace2Oligos.perl ++++ b/scripts/ace2Oligos.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # ace2Oligos.perl + # +@@ -16,6 +16,8 @@ + # Rev: 000330 to handle comments in oligo tags + # + ++use warnings; ++ + $szUsage = "Usage: ace2Oligos.perl (name of ace file) (name of oligo file)"; + + if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { +--- a/scripts/add454Reads.perl ++++ b/scripts/add454Reads.perl +@@ -1,11 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # add454Reads.perl + # part of Consed package + # + # DG with help from Hao Wang to screen vector + +- ++use warnings; + use File::Basename; + + +--- a/scripts/addReads2Consed.perl ++++ b/scripts/addReads2Consed.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Purpose: called by consed in order to add new reads to an + # existing assembly without reassemblying +@@ -29,6 +29,7 @@ + # Rev: 080320 (David Gordon) to use discrep_lists instead of alignments + # Rev: 130828 (David Gordon) to handle slashes (/) in read names + ++use warnings; + + $szVersion = "130828"; + if ( $#ARGV >= 0 ) { +--- a/scripts/addSangerReads.perl ++++ b/scripts/addSangerReads.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # addSangerReads.perl + +@@ -32,7 +32,7 @@ + # added is printed in a report ending with ".log". The name of this + # file is listed in auto.fof + +- ++use warnings; + + + $szVersion = "120717"; +--- a/scripts/addSolexaReads.perl ++++ b/scripts/addSolexaReads.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # addSolexaReads.perl + +@@ -54,7 +54,7 @@ + + $szUsage = "addSolexaReads.perl -ace (ace file) -fastqfof (solexa files) -fasta (fasta file) -readsList (file of list of desired reads) where -readsList is optional"; + +- ++use warnings; + use Getopt::Long; + + GetOptions( "ace=s" => \$szAceFile, +--- a/scripts/alignRNA2Genomic.perl ++++ b/scripts/alignRNA2Genomic.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # alignRNA2Genomic.perl + +@@ -6,6 +6,8 @@ + # consed-ready ace and phd ball with the RNA aligned against the + # genomic with introns being represented by large gaps + ++use warnings; ++ + $szVersion = "120717"; + + if ( $#ARGV == 0 ) { +--- a/scripts/alignSolexaReads2Refs.perl ++++ b/scripts/alignSolexaReads2Refs.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # Input: a file where each line looks like this: + # (solexa seq file) (read prefix) +@@ -10,6 +10,7 @@ + + # Output: a list of alignment files + ++use warnings; + + defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || + ( $szConsedHome = "/usr/local/genome" ); +--- a/scripts/amplifyTranscripts.perl ++++ b/scripts/amplifyTranscripts.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: runs consed -autoPCRAmplify in order to pick pcr primers + # for a large group of regions +@@ -40,7 +40,7 @@ + # That is, the left primers are given in top strand orientation, and + # the right primers are given in bottom strand orientation. + +- ++use warnings; + + defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || + ( $szConsedHome = "/usr/local/genome" ); +--- a/scripts/autoPrimers.perl ++++ b/scripts/autoPrimers.perl +@@ -1,5 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + ++use warnings; + + $szUsage = "autoPrimers.perl (fasta file of targets)"; + $szVersion = "141226"; +--- a/scripts/bam2Ace.perl ++++ b/scripts/bam2Ace.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + + # Purpose: runs: +@@ -6,6 +6,7 @@ + # 2) consed -renameDuplicates + # 3) consed -removeColumnsOfPads + ++use warnings; + + $szUsage = "usage: bam2Ace.perl -bamFile (bam file) -regionsFile (regions file) (see README.txt for format of the regions file) -exec (consed executable name) -newAceFile (new ace file name) where the -exec (exec) is optional"; + +--- a/scripts/convertBedToBamScape.perl ++++ b/scripts/convertBedToBamScape.perl +@@ -1,4 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + + $szUsage = "usage: convertBedToBamScape.perl (Bed file) (BamScape file) (fasta file of all sequences) (conversion of reference names--optional)"; + +--- a/scripts/countEditedBases.perl ++++ b/scripts/countEditedBases.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # countEditedBases.perl + # +@@ -11,6 +11,8 @@ + # + # + ++use warnings; ++ + while(<>) { + if ( /^CO / ) { + @aWords = split; +--- a/scripts/determineReadTypes.perl ++++ b/scripts/determineReadTypes.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # determineReadTypes.perl + # + # Purpose: to write into the phd file information about the template +@@ -173,6 +173,7 @@ + # + ############################################################### + ++use warnings; + + # you can remove or comment out this line when you are satisfied with + # your customized version of this file. +--- a/scripts/fasta2Ace.perl ++++ b/scripts/fasta2Ace.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # manyFasta2Ace.perl + # +@@ -13,6 +13,7 @@ + # + # NOTE: you must run this in edit_dir + ++use warnings; + use Getopt::Long; + + $szRevision = "141212"; +--- a/scripts/fasta2PhdBall.perl ++++ b/scripts/fasta2PhdBall.perl +@@ -1,4 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + + $nQuality = 20; + +--- a/scripts/fasta2Phd.perl ++++ b/scripts/fasta2Phd.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # fasta2Phd.perl + # +@@ -20,6 +20,7 @@ + # June 2002, Bill Gilliland to allow the user to specify + # the quality value + ++use warnings; + use Getopt::Long; + GetOptions( "quality=i" => \$qualityValue); + +--- a/scripts/fastq2Phrap.perl ++++ b/scripts/fastq2Phrap.perl +@@ -1,4 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + + $szUsage = "fastq2Phrap.perl (fastq) or for paired reads fastq2Phrap.perl (fastq1) (fastq2) where fastq1 and fastq2 have corresponding mate pairs--e.g., the 5th read in fastq1 is the mate of the 5th read in fastq2--these fastq files are assumed to be in ../solexa_dir--not the current directory\n"; + +--- a/scripts/filter454Reads.perl ++++ b/scripts/filter454Reads.perl +@@ -1,6 +1,6 @@ +-#!/usr/bin/perl -w +- ++#!/usr/bin/env perl + ++use warnings; + use File::Basename; + + +--- a/scripts/findSequenceMatchesForConsed.perl ++++ b/scripts/findSequenceMatchesForConsed.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # findSequenceMatchesForConsed.perl + +@@ -16,6 +16,8 @@ + # REVISIONS: 021127 (DG) to write (project).(date).(time).fasta instead of + # (project).fasta.screen.ace.1.(date).(time).fasta + ++use warnings; ++ + $szVersion = "021127"; + + $szUsage = "Usage: findSequenceMatchesForConsed.perl (ace file) (crossmatch parameters, if any)"; +--- a/scripts/fixContigEnd.perl ++++ b/scripts/fixContigEnd.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # fixContigEnd.perl + +@@ -7,6 +7,7 @@ + # consed -ace (acefile) -fixContigEnds + # + ++use warnings; + + $szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)"; + +--- a/scripts/lib2Phd.perl ++++ b/scripts/lib2Phd.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # lib2Phd.perl + # +@@ -23,6 +23,8 @@ + # accept fasta library files as input. The output file is named + # according to the first, non-space block of text on each fasta defline. + ++use warnings; ++ + $nQuality = 20; + + $szUsage = "Usage: lib2Phd.perl "; +--- a/scripts/makePhdBall.perl ++++ b/scripts/makePhdBall.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: concatenate all phd file into a single phd.ball + # for the purpose of fast startup of consed +@@ -9,6 +9,7 @@ + # + # February 2008, David Gordon + ++use warnings; + + if ( $#ARGV >= 0 ) { + if ( $ARGV[0] eq "-v" || $ARGV[0] eq "-V" ) { +--- a/scripts/makeRegionsFile.perl ++++ b/scripts/makeRegionsFile.perl +@@ -1,10 +1,12 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # makeRegionsFile.perl + # To be used with consed -bam2Ace + # Takes a fasta file of sequences and makes a regions file that + # specifies the entire length of each sequence. + ++use warnings; ++ + $szUsage = "makeRegionsFile.perl (name of fasta file)"; + + $szVersion = "110914"; +--- a/scripts/orderPrimerPairs.perl ++++ b/scripts/orderPrimerPairs.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: puts the primers in 96 well format for ordering. + # creates a file that can be emailed to +@@ -13,6 +13,8 @@ + # 2) a file of primer pairs, sorted by product size + # 3) a fasta file of the primers, for your convenience for analysis + ++use warnings; ++ + $| = 1; + + $szUsage = "orderPrimerPairs.perl"; +--- a/scripts/phd2Ace.perl ++++ b/scripts/phd2Ace.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # phd2Ace.perl + # +@@ -13,6 +13,8 @@ + # REV: 981002 (David Gordon) for new ace format + # 981210 (DG) to eliminate warning message + ++use warnings; ++ + $szPhdDirPath = "../phd_dir"; + + $szUsage = "Usage: phd2Ace.perl \nThe phd file is assumed to reside in $szPhdDirPath"; +--- a/scripts/phredPhrap ++++ b/scripts/phredPhrap +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # phredPhrap + # +@@ -70,6 +70,8 @@ + # Rev: 110609 to allow masking of vector sequence when doing miniassemblies + # Rev: 120312 to not duplicate consensus tags during miniassembly + ++use warnings; ++ + $szVersion = "120312"; + + +--- a/scripts/picard2Regions.perl ++++ b/scripts/picard2Regions.perl +@@ -1,10 +1,12 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: takes a file of locations in the format for bamScape custom + # navigation (Picard IntervalList format), adds 2000 bases of context + # to each side of each location, and prints a region file in format to + # be used by bam2Ace + ++use warnings; ++ + $szRevision = "140903"; # David Gordon + + if ( defined( $ARGV[0] ) && +--- a/scripts/removeReads ++++ b/scripts/removeReads +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # PURPOSE: removes a list of chromats from an assembly. After running this, + # you must reassemble to create an ace file without the given phd files. +@@ -16,6 +16,8 @@ + # removeReads (name of fof's) + # + ++use warnings; ++ + $szUsage = "Usage: removeReads listOfReads.fof"; + + die "$szUsage" if ( $#ARGV != 0 ); +--- a/scripts/revertToUneditedRead ++++ b/scripts/revertToUneditedRead +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # PURPOSE: If the user really screws up a read, to back out all changes. + # You must reassemble after using this. +@@ -16,6 +16,7 @@ + # REV: 7/24/98 (DG) + # REV: 8/28/2013 (DG) to handle readnames with slashes (/) + ++use warnings; + + $szUsage = "Usage: revertToUneditedRead (read name without any .phd.# extension)"; + +--- a/scripts/selectOneRegion.perl ++++ b/scripts/selectOneRegion.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # selectOneRegion.perl + # +@@ -11,6 +11,7 @@ + # and you will create an ace file chr15_51000000.ace or chr15_51000000.ace.1 + # (or higher extension) + ++use warnings; + use Getopt::Long; + + +--- a/scripts/selectRegions.perl ++++ b/scripts/selectRegions.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # selectRegions.perl + # +@@ -43,7 +43,7 @@ + # my_new_ace.ace says what the ace file should be called (the + # extension may not start at 1 if there is already a .1 + +- ++use warnings; + + $SIG{__WARN__} = dieWhenGetWarning; + sub dieWhenGetWarning { +--- a/scripts/tagRepeats.perl ++++ b/scripts/tagRepeats.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # PROGRAM: tagRepeats.perl + # PURPOSE: to put consensus tags on any found ALU or any other +@@ -10,6 +10,7 @@ + # INPUTS: The ace file. You must also provide a fasta file of the + # ALU or any other sequence you want to tag + ++use warnings; + + $szVersion = "090209"; + if ( $#ARGV >= 0 ) { +--- a/scripts/testSocket.perl ++++ b/scripts/testSocket.perl +@@ -1,7 +1,8 @@ +-#! /usr/local/bin/perl -w ++#!/usr/bin/env perl + + # open a socket to consed +- ++ ++use warnings; + use IO::Socket; + + # Consed makes a file which has nothing but the port number. +--- a/scripts/transferConsensusTags.perl ++++ b/scripts/transferConsensusTags.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Purpose: Transfers consensus tags from an old assembly to + # a new assembly. +@@ -44,6 +44,8 @@ + # Nov 2001, DG to handle cloneEnd tags which have orientation + # Mar 2012, DG to prevent duplicating tags after miniassembly + ++use warnings; ++ + $szUsage = "Usage: transferConsensusTags.perl (old ace file) (new ace file) (file of list of old contigs with consensus tags to be transferred)"; + + if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch new file mode 100644 index 000000000000..5bdf0264d25b --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-qa.patch @@ -0,0 +1,275 @@ +Fix various QA violations, due to +* implicit declarations +* incorrect printf() format specifiers +* incorrect function prototypes +* remove unsafe gets() fucntion + +--- a/misc/454/sff2scf.c ++++ b/misc/454/sff2scf.c +@@ -39,6 +39,7 @@ + void writeScfFile(char *filearg, char *outfile); + void writeScfCommand(char *filearg, char *outfile); + ++int sffinfo(int argc, char *argv[], FILE* pTempFile ); + + int main(int argc, char *argv[]) + { +--- a/misc/mktrace/mktrace.c ++++ b/misc/mktrace/mktrace.c +@@ -70,9 +70,9 @@ + else + { + printf( "enter FASTA filename: " ); +- gets( ifnm ); ++ fgets( ifnm, sizeof(ifnm), stdin ); + printf( "enter output filename: " ); +- gets( ofnm ); ++ fgets( ofnm, sizeof(ofnm), stdin ); + } + + /* +@@ -192,7 +192,7 @@ + /* + ** Write phd file. + */ +- if( writePhd( ofnm, numBase, seq, qual, pos, numPoint, trace ) == ERROR ) ++ if( writePhd( ofnm, numBase, seq, qual, pos, numPoint ) == ERROR ) + { + fprintf( stderr, "mktrace: error: bad status: writePhd\n" ); + free( seq ); +--- a/misc/mktrace/mktrace.h ++++ b/misc/mktrace/mktrace.h +@@ -37,8 +37,8 @@ + int writeSCF( char *filename, int numBase, char *seq, int numPoint, float **trace ); + int freeTrace( float **trace ); + char *readFASTA( char *filename, char *entryName, char *comments, int *len ); +-int writePhd( char *ofnm, int numBase, char *seq, int *pos, int numPoint ); + int *readQUAL( char *filename, char *entryName, char *comments, int *len ); ++char *getTime( void ); + #else + int writePhd(); + float **synTrace(); +--- a/misc/phd2fasta/phd2fasta.h ++++ b/misc/phd2fasta/phd2fasta.h +@@ -276,6 +276,10 @@ + Comments *comments, Seq *seq, TagList *tagList, char *emsg ); + int checkIntString( char *string ); + int delimiterTest( char *string, unsigned int mask ); ++int checkParam( Option *option ); ++char* getVersion( void ); ++int showDoc( void ); ++char* getTime( void ); + #else + Option *getOption(); + struct Tag *allocTag(); +--- a/misc/phd2fasta/readStdTag.c ++++ b/misc/phd2fasta/readStdTag.c +@@ -699,11 +699,11 @@ + if( fstat ) + { + fprintf( stderr, +- "readStdTag: %s: line: %d: unexpected delimiter %s\n", ++ "readStdTag: %s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", ++ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +--- a/misc/phd2fasta/readWholeReadTag.c ++++ b/misc/phd2fasta/readWholeReadTag.c +@@ -393,11 +393,11 @@ + if( fstat ) + { + fprintf( stderr, +- "readWholeReadTag: %s: line: %d: unexpected delimiter %s\n", ++ "readWholeReadTag: %s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", ++ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +--- a/misc/phd2fasta/writeFasta.c ++++ b/misc/phd2fasta/writeFasta.c +@@ -39,7 +39,7 @@ + #include "phd2fasta.h" + + #ifdef ANSI_C +-writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, ++int writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, + int outBasePosOption, + Comments *comments, Seq *seq, TagList *tagList, char *emsg ) + #else +--- a/motifutils.cpp ++++ b/motifutils.cpp +@@ -202,13 +202,13 @@ + void printButtonEvent( XButtonEvent* pEvent ) { + + printf( "type = %d\n", pEvent->type ); +- printf( "serial = %d\n", pEvent->serial ); ++ printf( "serial = %lu\n", pEvent->serial ); + printf( "send_event = %s\n", szPrintBool( pEvent->send_event ) ); +- printf( "*display = %x\n", pEvent->display ); +- printf( "window = %x\n", pEvent->window ); +- printf( "root = %x\n", pEvent->root ); +- printf( "subwindow = %x\n", pEvent->subwindow ); +- printf( "time = %d\n", pEvent->time ); ++ printf( "*display = %p\n", pEvent->display ); ++ printf( "window = %lu\n", pEvent->window ); ++ printf( "root = %lu\n", pEvent->root ); ++ printf( "subwindow = %lu\n", pEvent->subwindow ); ++ printf( "time = %lu\n", pEvent->time ); + printf( "x = %d\n", pEvent->x ); + printf( "y = %d\n", pEvent->y ); + printf( "x_root = %d\n", pEvent->x_root ); +--- a/phaster2PhdBall.cpp ++++ b/phaster2PhdBall.cpp +@@ -547,7 +547,7 @@ + + int nTokens = + sscanf( soLine_.data(), +- "%s %*s %d %d %lld %s %s %*s %d %d %lld %s %s\n", ++ "%s %*s %d %d %ld %s %s %*s %d %d %ld %s %s\n", + soReadName_.data(), + &nRead1Left_, + &nRead1Right_, +--- a/printAutoFinishMiscInfo.cpp ++++ b/printAutoFinishMiscInfo.cpp +@@ -80,7 +80,7 @@ + int nError = stat( (char*) soAceFileFullPathname.data(), &statBuffer ); + + if (nError == 0 ) { +- fprintf( pAO,"size: %d date: %s\n", ++ fprintf( pAO,"size: %ld date: %s\n", + (long) statBuffer.st_size, + ctime( &( statBuffer.st_mtime )) ); + +--- a/printAutoFinishParameters.cpp ++++ b/printAutoFinishParameters.cpp +@@ -206,7 +206,7 @@ + pCP->nInexactSearchForStringMaxPerCentMismatch_ ); + + fprintf( pAO, "! when using the inexact search for string, allow up to this\n"); +- fprintf( pAO, "! % mismatch: the sum of the insertion, deletion, and substitution\n"); ++ fprintf( pAO, "! %% mismatch: the sum of the insertion, deletion, and substitution\n"); + fprintf( pAO, "! differences divided by the length of the query string\n"); + fprintf( pAO, "! (YES)\n"); + fprintf( pAO, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n", +@@ -825,7 +825,7 @@ + fprintf( pAO, "! template will be 1500 bases from the forward read. But if this template\n"); + fprintf( pAO, "! has an insert that is shorter than average, the walk may walk into vector.\n"); + fprintf( pAO, "! To be conservative, we may want to assume that the insert is somewhat \n"); +- fprintf( pAO, "! shorter than average. By default, we assume that it is 90% as large as \n"); ++ fprintf( pAO, "! shorter than average. By default, we assume that it is 90%% as large as \n"); + fprintf( pAO, "! the average. This parameter gives that percentage. This parameter\n"); + fprintf( pAO, "! is used both by Consed and Autofinish.\n"); + fprintf( pAO, "! (OK)\n"); +@@ -1249,9 +1249,9 @@ + pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); + + fprintf( pAO, "! Autofinish computes the per cent of existing reads are aligned at\n"); +- fprintf( pAO, "! each base position. Typically, this number starts at around 0% at\n"); +- fprintf( pAO, "! base position 1, rises to close to 100% at around base position 300,\n"); +- fprintf( pAO, "! and then drops again to 0% at base position 800 or so. This number\n"); ++ fprintf( pAO, "! each base position. Typically, this number starts at around 0%% at\n"); ++ fprintf( pAO, "! base position 1, rises to close to 100%% at around base position 300,\n"); ++ fprintf( pAO, "! and then drops again to 0%% at base position 800 or so. This number\n"); + fprintf( pAO, "! specifies how high the number must be for Autofinish to consider an\n"); + fprintf( pAO, "! Autofinish read to cover a single subclone region.\n"); + fprintf( pAO, "! (OK)\n"); +@@ -1295,7 +1295,7 @@ + ( ( pCP->bCheckIfTooManyWalks_ ) ? "true" : "false" ) ); + + fprintf( pAO, "! this just checks if the number of walks, pcr ends, and unknown reads\n"); +- fprintf( pAO, "! exceeds 20% of the total number of reads. If this is exceeded, then \n"); ++ fprintf( pAO, "! exceeds 20%% of the total number of reads. If this is exceeded, then \n"); + fprintf( pAO, "! a warning message is given. Typically, such a warning indicates\n"); + fprintf( pAO, "! that you have incorrectly customized determineReadTypes.perl\n"); + fprintf( pAO, "! (OK)\n"); +@@ -1446,7 +1446,7 @@ + ( ( pCP->bProcessMatePairsAtStartup_ ) ? "true" : "false" ) ); + + fprintf( pAO, "! This is necessary to show the mate pair flags, but it does add\n"); +- fprintf( pAO, "! around 15% to startup time.\n"); ++ fprintf( pAO, "! around 15%% to startup time.\n"); + fprintf( pAO, "! (OK)\n"); + fprintf( pAO, "consed.maximumNumberOfTracesShown: %d\n", + pCP->nMaximumNumberOfTracesShown_ ); +@@ -1796,7 +1796,7 @@ + (char*)pCP->soStoreTracePeakPositions_.data() ); + + fprintf( pAO, "! never, always or whenChromatAvailable\n"); +- fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%,\n"); ++ fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%%,\n"); + fprintf( pAO, "! especially if the assembler is Newbler. always means it will store\n"); + fprintf( pAO, "! the positions if they are present in the phd file/ball.\n"); + fprintf( pAO, "! \"whenChromatAvailable\" means it will store trace peak positions for\n"); +--- a/readPrimerScreenSequences.cpp ++++ b/readPrimerScreenSequences.cpp +@@ -167,7 +167,7 @@ + ++nSequenceNumber ) { + if ( pnLengthOfSequence[ nSequenceNumber ] != + strlen( pszSequence[ nSequenceNumber ] ) ) { +- sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %d for sequence number %d", ++ sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %zu for sequence number %d", + pnLengthOfSequence[ nSequenceNumber ], + strlen( pszSequence[ nSequenceNumber ] ), + nSequenceNumber ); +--- a/rwcstring.cpp ++++ b/rwcstring.cpp +@@ -235,7 +235,7 @@ + + nMaxLength_ = nDefaultLengthForConversions; + +- nCurrentLength_ = sprintf( sz_, "%d", lNumberToConvert ); ++ nCurrentLength_ = sprintf( sz_, "%ld", lNumberToConvert ); + + if ( nCurrentLength_ > nMaxLength_ ) { + // big trouble--might not even make it here--might segmentation fault +--- a/someOtherProgramSentACommandToConsed.cpp ++++ b/someOtherProgramSentACommandToConsed.cpp +@@ -89,7 +89,7 @@ + + char szLine2[ nMaxLine ]; + +- sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine ); ++ sprintf( szLine2, "# of chars = %zu %s", strlen( szLine ), szLine ); + + cout << szLine2 << endl; + +--- a/tag.cpp ++++ b/tag.cpp +@@ -466,7 +466,7 @@ + fprintf( pPhdFile, "DATE: %s\n", soDate_.data() ); + + if ( lID_ != nUndefinedTagID ) { +- fprintf( pPhdFile, "ID: %d\n", lID_ ); ++ fprintf( pPhdFile, "ID: %ld\n", lID_ ); + } + + +--- a/userDefinedTagField.cpp ++++ b/userDefinedTagField.cpp +@@ -64,7 +64,7 @@ + + void userDefinedIntegerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { + +- fprintf( pFile, "%s %d\n", ++ fprintf( pFile, "%s %ld\n", + pUserDefinedTagFieldType_->soFieldName_.data(), + l_ ); + } +@@ -119,7 +119,7 @@ + + void userDefinedPointerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { + +- fprintf( pFile, "%s %d\n", ++ fprintf( pFile, "%s %ld\n", + pUserDefinedTagFieldType_->soFieldName_.data(), + lID_ ); + diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/consed/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + -- cgit v1.2.3