From owner-dev-commits-ports-all@freebsd.org Tue Jun 22 17:58:04 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id AC3AB660AD7; Tue, 22 Jun 2021 17:58:04 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4G8Yz04Cp9z3Lp0; Tue, 22 Jun 2021 17:58:04 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 787481570D; Tue, 22 Jun 2021 17:58:04 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 15MHw4VH061201; Tue, 22 Jun 2021 17:58:04 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 15MHw4et061199; Tue, 22 Jun 2021 17:58:04 GMT (envelope-from git) Date: Tue, 22 Jun 2021 17:58:04 GMT Message-Id: <202106221758.15MHw4et061199@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 69656bf0d7d9 - main - biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 69656bf0d7d99660e536c22472a5eae639695a97 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 22 Jun 2021 17:58:04 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=69656bf0d7d99660e536c22472a5eae639695a97 commit 69656bf0d7d99660e536c22472a5eae639695a97 Author: Jason W. Bacon AuthorDate: 2021-06-22 17:55:15 +0000 Commit: Jason W. Bacon CommitDate: 2021-06-22 17:55:15 +0000 biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives SRA tools is a toolkit for using data in the INSDC Sequence Read Archives. SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by "next-gen" sequencers. This port is a bit convoluted due to the fact that the sra-tools build requires access to the ncbi-vdb source tree. Hence, ncbi-vdb is treated as a submodule here rather than a separate library port. We are working with upstream with hope for long-term improvements. --- biology/Makefile | 1 + biology/sra-tools/Makefile | 105 +++++++ biology/sra-tools/distinfo | 7 + biology/sra-tools/files/Makefile.bsd | 72 +++++ biology/sra-tools/files/byteswap.h | 40 +++ biology/sra-tools/files/ld.bsd.clang.sh | 47 +++ biology/sra-tools/files/ld.bsd.cmn.sh | 158 ++++++++++ biology/sra-tools/files/ld.bsd.dlib.sh | 308 +++++++++++++++++++ biology/sra-tools/files/ld.bsd.exe.sh | 326 +++++++++++++++++++++ biology/sra-tools/files/ld.bsd.gcc.sh | 47 +++ biology/sra-tools/files/ld.bsd.ln.sh | 98 +++++++ biology/sra-tools/files/ld.bsd.slib.sh | 146 +++++++++ .../sra-tools/files/patch-build_ld.linux.exe.sh | 11 + .../files/patch-ncbi-vdb_build_Makefile.clang | 30 ++ .../files/patch-ncbi-vdb_build_Makefile.env | 25 ++ .../files/patch-ncbi-vdb_build_Makefile.gcc | 35 +++ .../files/patch-ncbi-vdb_build_Makefile.install | 11 + .../files/patch-ncbi-vdb_build_Makefile.shell | 31 ++ .../patch-ncbi-vdb_interfaces_os_sun_atomic32.h | 85 ++++++ .../files/patch-ncbi-vdb_libs_ext_Makefile | 12 + .../files/patch-ncbi-vdb_libs_kfg_config.c | 20 ++ .../files/patch-ncbi-vdb_libs_klib_unix_systime.c | 11 + .../files/patch-ncbi-vdb_libs_kns_unix_syssock.c | 10 + .../files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile | 20 ++ .../files/patch-ncbi-vdb_libs_search_Makefile | 12 + .../files/patch-ncbi-vdb_setup_konfigure.perl | 243 +++++++++++++++ .../files/patch-ncbi-vdb_setup_os-arch.prl | 20 ++ .../files/patch-ncbi-vdb_test_kapp_run-sig-core.sh | 49 ++++ .../files/patch-ncbi-vdb_test_kfg_kfgtest.cpp | 11 + .../files/patch-ncbi-vdb_test_klib_printf-test.c | 11 + .../files/patch-ncbi-vdb_test_kns_Makefile | 19 ++ .../patch-ncbi-vdb_test_vdb_test-dependencies.cpp | 11 + ...s_redirect-rejected-names-cgi-http-to-https.cpp | 11 + biology/sra-tools/files/patch-setup_install.perl | 13 + biology/sra-tools/files/patch-setup_konfigure.perl | 121 ++++++++ .../files/patch-tools_bam-loader_loader-imp.c | 10 + .../sra-tools/files/patch-tools_copycat_Makefile | 11 + .../files/patch-tools_driver-tool_Makefile | 16 + .../files/patch-tools_driver-tool_cmdline.cpp | 13 + .../patch-tools_driver-tool_utf8proc_Makefile | 11 + .../patch-tools_fastq-loader_spot-assembler.c | 11 + .../sra-tools/files/patch-tools_sra-sort_Makefile | 13 + .../files/patch-tools_util_validate-names4.c | 13 + biology/sra-tools/pkg-descr | 18 ++ biology/sra-tools/pkg-plist | 57 ++++ 45 files changed, 2350 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index ec9728ced8ee..158eb70ede1a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -175,6 +175,7 @@ SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa + SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile new file mode 100644 index 000000000000..0b6a54bd67ca --- /dev/null +++ b/biology/sra-tools/Makefile @@ -0,0 +1,105 @@ +PORTNAME= sra-tools +DISTVERSION= 2.11.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives + +LICENSE= PD LGPL21+ +LICENSE_COMB= multi +LICENSE_FILE_PD= ${WRKSRC}/LICENSE +LICENSE_DISTFILES_LGPL21+ = + +ONLY_FOR_ARCHS= amd64 +ONLY_FOR_ARCHS_REASON= NCBI-VDB requires SSE2 instructions, no 32-bit support + +BUILD_DEPENDS= bash:shells/bash \ + ${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk +LIB_DEPENDS= libxml2.so:textproc/libxml2 \ + libhdf5.so:science/hdf5 \ + libepoll-shim.so:devel/libepoll-shim + +USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix +USE_PERL5= build +USE_GITHUB= yes + +SHEBANG_GLOB= *.sh *.pl +GH_ACCOUNT= ncbi +GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs/ngs # ported as biology/ngs-sdk +GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb + +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --with-ngs-sdk-prefix=${LOCALBASE} \ + --with-ncbi-vdb-sources=${NCBI_VDB_WRKSRC} \ + --with-xml2-prefix=${LOCALBASE} \ + --with-hdf5-prefix=${LOCALBASE} \ + CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" \ + --with-ncbi-vdb-build=${NCBI_VDB_WRKSRC}/amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) +MAKE_ARGS= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \ + INST_ETCDIR=${STAGEDIR}${PREFIX}/etc + +NCBI_VDB_WRKSRC= ${WRKSRC}/ncbi-vdb +NCBI_VDB_FILESDIR= ${FILESDIR} +FREEBSD_RELEASE= uname -r | cut -d - -f 1 + +CFLAGS+= -I${WRKSRC}/interfaces/os/sun +CXXFLAGS+= -I${WRKSRC}/interfaces/os/sun + +BINARY_ALIAS= gcc=${CC} g++=${CXX} + +# for port developers, building with these options may fail +OPTIONS_DEFINE= DEBUG OPTIMIZED_CFLAGS TEST +DEBUG_PREVENTS= OPTIMIZED_CFLAGS +DEBUG_CONFIGURE_WITH= debug +OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT="" +TEST_TEST_TARGET= test +TEST_USES= python + +# ncbi-vdb build extras +VDB_CONFIGURE_ARGS= \ + --with-xml2-prefix=${LOCALBASE} \ + --with-hdf5-prefix=${LOCALBASE} \ + --prefix=${PREFIX} \ + --build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \ + CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" +VDB_MAKE_ARGS+= -j 1 CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" +MAKE_ENV+= CPATH="${LOCALBASE}/include/libepoll-shim" +CFLAGS+= -I${WRKSRC}/lib + +pre-patch: + @${CP} ${FILESDIR}/Makefile.bsd ${NCBI_VDB_WRKSRC}/build/ + @${CP} ${FILESDIR}/ld.bsd.*.sh ${NCBI_VDB_WRKSRC}/build/ + @${MKDIR} ${NCBI_VDB_WRKSRC}/interfaces/os/bsd + @${CP} -p ${NCBI_VDB_WRKSRC}/interfaces/os/mac/endian.h \ + ${NCBI_VDB_WRKSRC}/interfaces/os/bsd/ + +post-patch: + @${GREP} -q '@@PREFIX@@' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1) + @${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c + @${LN} -s ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64 + +post-patch-TEST-on: + @${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile + +pre-configure: + @${CP} ${NCBI_VDB_WRKSRC}/setup/os-arch.prl ${WRKSRC}/setup/os-arch.prl + # same as in biology/ncbi-vdb + @${CP} ${NCBI_VDB_FILESDIR}/Makefile.bsd ${WRKSRC}/build/ + @${CP} ${NCBI_VDB_WRKSRC}/build/ld.bsd.*.sh ${WRKSRC}/build/ + @${MKDIR} ${WRKSRC}/interfaces/override + @${CP} ${NCBI_VDB_WRKSRC}/interfaces/os/sun/atomic32.h ${WRKSRC}/interfaces/override + @${CP} ${FILESDIR}/byteswap.h ${WRKSRC}/interfaces/override + @cd ${WRKSRC}/ncbi-vdb && ./configure ${VDB_CONFIGURE_ARGS} + @${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/ncbi-vdb/build/COMP + @cd ${WRKSRC}/ncbi-vdb && ${DO_MAKE_BUILD} ${VDB_MAKE_ARGS} + +post-build-TEST-on: do-test + +do-install: + cd ${WRKSRC}/amd64-portbld-freebsd*/sra-tools/bsd/clang/*/rel/bin && \ + for f in `ls *.${PORTVERSION}`; do \ + ${INSTALL_PROGRAM} $${f} \ + ${STAGEDIR}${PREFIX}/bin/`basename $${f%%.${PORTVERSION}}`; \ + done + +.include diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo new file mode 100644 index 000000000000..fa75acf23fe6 --- /dev/null +++ b/biology/sra-tools/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1624382289 +SHA256 (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810 +SIZE (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 8966605 +SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc +SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365 +SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa +SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539 diff --git a/biology/sra-tools/files/Makefile.bsd b/biology/sra-tools/files/Makefile.bsd new file mode 100644 index 000000000000..7692ec277948 --- /dev/null +++ b/biology/sra-tools/files/Makefile.bsd @@ -0,0 +1,72 @@ +# =========================================================================== +# +# PUBLIC DOMAIN NOTICE +# National Center for Biotechnology Information +# +# This software/database is a "United States Government Work" under the +# terms of the United States Copyright Act. It was written as part of +# the author's official duties as a United States Government employee and +# thus cannot be copyrighted. This software/database is freely available +# to the public for use. The National Library of Medicine and the U.S. +# Government have not placed any restriction on its use or reproduction. +# +# Although all reasonable efforts have been taken to ensure the accuracy +# and reliability of the software and data, the NLM and the U.S. +# Government do not and cannot warrant the performance or results that +# may be obtained by using this software or data. The NLM and the U.S. +# Government disclaim all warranties, express or implied, including +# warranties of performance, merchantability or fitness for any particular +# purpose. +# +# Please cite the author in any work or product based on this material. +# +# =========================================================================== + + +# default compiler +ifeq (,$(COMP)) + COMP = clang +endif + +# handle attempts to set cross-compilation architecture +# note that if your installation is set up for cross compilation, +# you can try to enable it on your own. +ifeq (i386,$(ARCH)) +i386: + @ true +x86_64: + @ echo "FreeBSD builds do not support cross-compilation to this architecture" +endif + +ifeq (x86_64,$(ARCH)) +i386: + @ echo "FreeBSD builds do not support cross-compilation to this architecture" +x86_64: + @ true +endif + +.PHONY: i386 x86_64 + + +# library prefix +LPFX = lib + +# file extensions +OBJX = o +LOBX = pic.o +LIBX = a +SHLX = so + +# compilation defines +DEFINES := -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS) + +# FreeBSD is a Unix variant; for most cases, linux sources do well +OS_DAD = linux +OS_GDAD = unix + +# flex+bison: on Mac, use source-controlled generated .c/.h files +YACC = @ true +LEX = @ true + +# build matrix +COMPILERS = CLANG GCC diff --git a/biology/sra-tools/files/byteswap.h b/biology/sra-tools/files/byteswap.h new file mode 100644 index 000000000000..ef07fe98db64 --- /dev/null +++ b/biology/sra-tools/files/byteswap.h @@ -0,0 +1,40 @@ +/*=========================================================================== +* +* PUBLIC DOMAIN NOTICE +* National Center for Biotechnology Information +* +* This software/database is a "United States Government Work" under the +* terms of the United States Copyright Act. It was written as part of +* the author's official duties as a United States Government employee and +* thus cannot be copyrighted. This software/database is freely available +* to the public for use. The National Library of Medicine and the U.S. +* Government have not placed any restriction on its use or reproduction. +* +* Although all reasonable efforts have been taken to ensure the accuracy +* and reliability of the software and data, the NLM and the U.S. +* Government do not and cannot warrant the performance or results that +* may be obtained by using this software or data. The NLM and the U.S. +* Government disclaim all warranties, express or implied, including +* warranties of performance, merchantability or fitness for any particular +* purpose. +* +* Please cite the author in any work or product based on this material. +* +* =========================================================================== +* +*/ + +#ifndef _h_byteswap_ +#define _h_byteswap_ + +#include +#include + +/* N.B. Sun's BSWAP seems to be macro-based, + meaning that (x) will be evaluated multiple times */ + +#define bswap_16(x) bswap16 (x) +#define bswap_32(x) bswap32 (x) +#define bswap_64(x) bswap64 (x) + +#endif /* _h_byteswap_ */ diff --git a/biology/sra-tools/files/ld.bsd.clang.sh b/biology/sra-tools/files/ld.bsd.clang.sh new file mode 100755 index 000000000000..61c7779adcf1 --- /dev/null +++ b/biology/sra-tools/files/ld.bsd.clang.sh @@ -0,0 +1,47 @@ +#!/usr/local/bin/bash +# =========================================================================== +# +# PUBLIC DOMAIN NOTICE +# National Center for Biotechnology Information +# +# This software/database is a "United States Government Work" under the +# terms of the United States Copyright Act. It was written as part of +# the author's official duties as a United States Government employee and +# thus cannot be copyrighted. This software/database is freely available +# to the public for use. The National Library of Medicine and the U.S. +# Government have not placed any restriction on its use or reproduction. +# +# Although all reasonable efforts have been taken to ensure the accuracy +# and reliability of the software and data, the NLM and the U.S. +# Government do not and cannot warrant the performance or results that +# may be obtained by using this software or data. The NLM and the U.S. +# Government disclaim all warranties, express or implied, including +# warranties of performance, merchantability or fitness for any particular +# purpose. +# +# Please cite the author in any work or product based on this material. +# +# =========================================================================== + +# define linker params +LD_EXPORT_GLOBAL="-Wl,--export-dynamic" +LD_MULTIPLE_DEFS="-Wl,-zmuldefs" +LD_STATIC="-Wl,-Bstatic" +LD_DYNAMIC="-Wl,-Bdynamic" +LD_ALL_SYMBOLS="-Wl,-whole-archive" +LD_REF_SYMBOLS="-Wl,-no-whole-archive" + +# build command +DLIB_CMD="$LD -shared" +EXE_CMD="$LD" + +# versioned output +if [ "$VERS" = "" ] +then + DLIB_CMD="$DLIB_CMD -o $TARG" + EXE_CMD="$EXE_CMD -o $TARG" +else + set-vers $(echo $VERS | tr '.' ' ') + DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" + EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" +fi diff --git a/biology/sra-tools/files/ld.bsd.cmn.sh b/biology/sra-tools/files/ld.bsd.cmn.sh new file mode 100755 index 000000000000..a0a65f39884b --- /dev/null +++ b/biology/sra-tools/files/ld.bsd.cmn.sh @@ -0,0 +1,158 @@ +#!/usr/local/bin/bash +# =========================================================================== +# +# PUBLIC DOMAIN NOTICE +# National Center for Biotechnology Information +# +# This software/database is a "United States Government Work" under the +# terms of the United States Copyright Act. It was written as part of +# the author's official duties as a United States Government employee and +# thus cannot be copyrighted. This software/database is freely available +# to the public for use. The National Library of Medicine and the U.S. +# Government have not placed any restriction on its use or reproduction. +# +# Although all reasonable efforts have been taken to ensure the accuracy +# and reliability of the software and data, the NLM and the U.S. +# Government do not and cannot warrant the performance or results that +# may be obtained by using this software or data. The NLM and the U.S. +# Government disclaim all warranties, express or implied, including +# warranties of performance, merchantability or fitness for any particular +# purpose. +# +# Please cite the author in any work or product based on this material. +# +# =========================================================================== + +# script name +SELF_NAME="$(basename $0)" + +# parameters +LD="$1" +ARCH="$2" +BUILD="$3" +shift 3 + +SRCDIR="$1" +BINDIR="$2" +OUTDIR="$3" +TARG="$4" +NAME="$5" +DBGAP="$6" +shift 6 + +VERS="$1" +VERSFILE="$2" +DEPFILE="$3" +shift 3 + +MODE="$1" +SCMFLAGS="$2" +LDFLAGS="$3" +shift 3 + +LDIRS="$1" +XDIRS="$2" +shift 2 + +OBJS="$1" +LIBS="$2" + +# decode MODE +STATIC=$(expr $MODE % 2) +MODE=$(expr $MODE / 2) +DYLD=$(expr $MODE % 2) +MODE=$(expr $MODE / 2) +KPROC=$(expr $MODE % 2) +MODE=$(expr $MODE / 2) +THREADS=$(expr $MODE % 2) +MODE=$(expr $MODE / 2) +HAVE_M=$(expr $MODE % 2) +MODE=$(expr $MODE / 2) +HAVE_XML=$(expr $MODE % 2) + +# decode SCMFLAGS +CHECKSUM=$(expr $SCMFLAGS % 2) +STATICSYSLIBS=$(expr $SCMFLAGS / 2) + +# return parameter for find-lib +LIBPATH='' + +# initial command state +CMD='' +LD_STATIC_STATE=0 +LD_ALL_STATE=0 + +# for breaking out version +set-vers () +{ + MAJ=$1 + MIN=$2 + REL=$3 +} + +# for locating libraries +find-lib () +{ + _lib="lib$1" + _dirs="$2" + + LIBPATH='' + + while [ "$_dirs" != "" ] + do + _dir="${_dirs%%:*}" + + if [ "$_dir" != "" ] + then + if [ -e "$_dir/$_lib" ] + then + while [ -L "$_dir/$_lib" ] + do + _lib=$(readlink -n "$_dir/$_lib") + done + LIBPATH="$_dir/$_lib" + break; + fi + fi + + _dirs="${_dirs#$_dir}" + _dirs="${_dirs#:}" + done +} + +# setting state +load-static () +{ + if [ $LD_STATIC_STATE -eq 0 ] + then + CMD="$CMD $LD_STATIC" + LD_STATIC_STATE=1 + fi +} + +load-dynamic () +{ + if [ $LD_STATIC_STATE -eq 1 ] + then + CMD="$CMD $LD_DYNAMIC" + LD_STATIC_STATE=0 + fi +} + +load-all-symbols () +{ + if [ $LD_ALL_STATE -eq 0 ] + then + CMD="$CMD $LD_ALL_SYMBOLS" + LD_ALL_STATE=1 + fi +} + +load-ref-symbols () +{ + if [ $LD_ALL_STATE -eq 1 ] + then + CMD="$CMD $LD_REF_SYMBOLS" + LD_ALL_STATE=0 + fi +} diff --git a/biology/sra-tools/files/ld.bsd.dlib.sh b/biology/sra-tools/files/ld.bsd.dlib.sh new file mode 100755 index 000000000000..a74f2b006818 --- /dev/null +++ b/biology/sra-tools/files/ld.bsd.dlib.sh @@ -0,0 +1,308 @@ +#!/usr/local/bin/bash +# =========================================================================== +# +# PUBLIC DOMAIN NOTICE +# National Center for Biotechnology Information +# +# This software/database is a "United States Government Work" under the +# terms of the United States Copyright Act. It was written as part of +# the author's official duties as a United States Government employee and +# thus cannot be copyrighted. This software/database is freely available +# to the public for use. The National Library of Medicine and the U.S. +# Government have not placed any restriction on its use or reproduction. +# +# Although all reasonable efforts have been taken to ensure the accuracy +# and reliability of the software and data, the NLM and the U.S. +# Government do not and cannot warrant the performance or results that +# may be obtained by using this software or data. The NLM and the U.S. +# Government disclaim all warranties, express or implied, including +# warranties of performance, merchantability or fitness for any particular +# purpose. +# +# Please cite the author in any work or product based on this material. +# +# =========================================================================== + + +# =========================================================================== +# input library types, and their handling +# +# normal linkage +# -l : find shared or static +# -s : require static +# -d : require shared +# +# static linkage +# -l : require static +# -s : require static +# -d : ignore +# =========================================================================== + + +# script name +SELF_NAME="$(basename $0)" +BUILD_DIR="$(dirname $0)" + +# parameters and common functions +source "${0%dlib.sh}cmn.sh" + +# discover tool chain +case "$LD" in +g*) + source "${0%dlib.sh}gcc.sh" + ;; +c*) + source "${0%dlib.sh}clang.sh" + ;; + *) + echo "$SELF_NAME: unrecognized ld tool - '$LD'" + exit 5 +esac + +# DLIB_CMD was started in tool-specific source +CMD="$DLIB_CMD $LDFLAGS" + +# tack on object files +CMD="$CMD $OBJS" + +# list of static libraries used to create dynamic lib +SLIBS='' + +# initial dependency upon Makefile and vers file +DEPS="$SRCDIR/Makefile" +if [ "$LIBS" != "" ] +then + # tack on paths + DIRS="$LDIRS:$XDIRS" + while [ "$DIRS" != "" ] + do + DIR="${DIRS%%:*}" + [ "$DIR" != "" ] && CMD="$CMD -L$DIR" + DIRS="${DIRS#$DIR}" + DIRS="${DIRS#:}" + done + + # update LD_LIBRARY_PATH + unset LD_LIBRARY_PATH + export LD_LIBRARY_PATH="$LDIRS:$XDIRS" + + # tack on libraries, finding as we go + for LIB in $LIBS + do + + # strip off switch + LIBNAME="${LIB#-[lsd]}" + + # look at linkage + case "$LIB" in + -ldl|-ddl) + + # always load libdl as shared library + load-ref-symbols + load-dynamic +# CMD="$CMD -ldl" + ;; + + -l*) + + # normal or dynamic linkage + FOUND=0 + if [ $STATIC -eq 0 ] + then + find-lib $LIBNAME.so $LDIRS + if [ "$LIBPATH" != "" ] + then + + # found it + FOUND=1 + + # load normally + load-ref-symbols + load-dynamic + CMD="$CMD -l$LIBNAME" + + fi + fi + + # try static only + if [ $FOUND -eq 0 ] + then + find-lib $LIBNAME.a $LDIRS + if [ "$LIBPATH" != "" ] + then + + # found it + FOUND=1 + + # add it to dependencies + DEPS="$DEPS $LIBPATH" + SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" + + # load static + load-static + load-all-symbols + CMD="$CMD -l$LIBNAME" + + fi + fi + + # not found within our directories + if [ $FOUND -eq 0 ] + then + + if [ $STATICSYSLIBS -eq 1 ] + then + case "$LIBNAME" in + z|bz2) + # set load to static + load-static + load-all-symbols + ;; + + *) + # set load to dynamic + load-ref-symbols + load-dynamic + ;; + + esac + else + # set load to normal + load-ref-symbols + load-dynamic + fi + + CMD="$CMD -l$LIBNAME" + fi + ;; + + -s*) + + # force static load + FOUND=0 + find-lib $LIBNAME.a $LDIRS + if [ "$LIBPATH" != "" ] + then + + # found it + FOUND=1 + + # add it to dependencies + DEPS="$DEPS $LIBPATH" + SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" + + # load static + load-static + load-all-symbols + CMD="$CMD -l$LIBNAME" + + fi + + # not found within our directories + if [ $FOUND -eq 0 ] + then + + if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ] + then + # set load to static + load-static + load-all-symbols + else + + case "$LIBNAME" in + z|bz2) + # set load to dynamic + load-ref-symbols + load-dynamic + ;; + + *) + # set load to static + load-static + load-all-symbols + ;; + esac + fi + + CMD="$CMD -l$LIBNAME" + fi + ;; + + -d*) + + # only dynamic linkage + FOUND=0 + if [ $STATIC -eq 0 ] + then + find-lib $LIBNAME.so $LDIRS + if [ "$LIBPATH" != "" ] + then + + # found it + FOUND=1 + + # load normally + load-ref-symbols + load-dynamic + CMD="$CMD -l$LIBNAME" + + fi + fi + + # not found within our directories + if [ $FOUND -eq 0 ] + then + # set load to normal + load-ref-symbols + load-dynamic + CMD="$CMD -l$LIBNAME" + fi + ;; + + esac + + done +fi + +# put state back to normal +load-ref-symbols +load-dynamic + +# add in pthreads +if [ $THREADS -ne 0 ] +then + CMD="$CMD -lpthread" +fi + +# add in xml +if [ $HAVE_XML -ne 0 ] +then + CMD="$CMD -lxml2" +fi + +# add in math library +if [ $HAVE_M -ne 0 ] +then + CMD="$CMD -lm" +fi + +# produce shared library +echo "$CMD" +$CMD || exit $? + +# produce dependencies +if [ "$DEPFILE" != "" ] +then + echo "$TARG: $DEPS" > "$DEPFILE" +fi + +if [ $CHECKSUM -eq 1 ] +then + SCM_DIR="${BUILD_DIR%/*}/scm" + LOGFILE="$SCM_DIR/scm.log" + MSG=">>>>> scm: calling the collect script from ld.linux.dlib.sh <<<<<<" + #echo "$MSG" + echo "$MSG" >> $LOGFILE + + "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" +fi diff --git a/biology/sra-tools/files/ld.bsd.exe.sh b/biology/sra-tools/files/ld.bsd.exe.sh new file mode 100755 index 000000000000..650a212780c3 --- /dev/null +++ b/biology/sra-tools/files/ld.bsd.exe.sh @@ -0,0 +1,326 @@ +#!/usr/local/bin/bash +# =========================================================================== +# +# PUBLIC DOMAIN NOTICE +# National Center for Biotechnology Information +# +# This software/database is a "United States Government Work" under the +# terms of the United States Copyright Act. It was written as part of +# the author's official duties as a United States Government employee and +# thus cannot be copyrighted. This software/database is freely available +# to the public for use. The National Library of Medicine and the U.S. +# Government have not placed any restriction on its use or reproduction. +# +# Although all reasonable efforts have been taken to ensure the accuracy +# and reliability of the software and data, the NLM and the U.S. +# Government do not and cannot warrant the performance or results that +# may be obtained by using this software or data. The NLM and the U.S. +# Government disclaim all warranties, express or implied, including +# warranties of performance, merchantability or fitness for any particular +# purpose. +# +# Please cite the author in any work or product based on this material. +# +# =========================================================================== + + +# =========================================================================== +# input library types, and their handling +# +# normal linkage +# -l : find shared or static +# -s : require static +# -d : ignore - will be dynamically loaded +# +# static linkage +# -l : require static +# -s : require static +# -d : require static +# =========================================================================== + + +# script name +SELF_NAME="$(basename $0)" +BUILD_DIR="$(dirname $0)" + +# parameters and common functions +source "${0%exe.sh}cmn.sh" + +# discover tool chain +case "$LD" in +g*) + source "${0%exe.sh}gcc.sh" + ;; +c*) + source "${0%exe.sh}clang.sh" + ;; +*) + echo "$SELF_NAME: unrecognized ld tool - '$LD'" + exit 5 +esac + +# EXE_CMD was started in tool-specific source +CMD="$EXE_CMD $LDFLAGS" + +# if building a static executable against dynamic libraries +# the main application will substitute for name lookup +if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ] +then +# CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS" + CMD="$CMD $LD_EXPORT_GLOBAL" +fi + +# tack on object files +CMD="$CMD $OBJS" + +# list of static libraries used to create executable +SLIBS='' + +# initial dependency upon Makefile and vers file +DEPS="$SRCDIR/Makefile $VERSFILE" +if [ "$LIBS" != "" ] +then + # tack on paths + DIRS="$LDIRS:$XDIRS" + while [ "$DIRS" != "" ] + do + DIR="${DIRS%%:*}" + [ "$DIR" != "" ] && CMD="$CMD -L$DIR" + DIRS="${DIRS#$DIR}" + DIRS="${DIRS#:}" + done + + # update LD_LIBRARY_PATH + unset LD_LIBRARY_PATH + export LD_LIBRARY_PATH="$LDIRS:$XDIRS" + + # tack on libraries, finding as we go + for LIB in $LIBS + do + + # strip off switch + LIBNAME="${LIB#-[lsd]}" + + # look at linkage + case "$LIB" in + -ldl|-ddl) + + # always load libdl as shared library + load-ref-symbols + load-dynamic +# CMD="$CMD -ldl" + ;; + + -l*) + + # normal or dynamic linkage + FOUND=0 + if [ $STATIC -eq 0 ] + then + find-lib $LIBNAME.so $LDIRS + if [ "$LIBPATH" != "" ] *** 1707 LINES SKIPPED ***