git: 69656bf0d7d9 - main - biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives
Jason W. Bacon
jwb at FreeBSD.org
Tue Jun 22 17:58:04 UTC 2021
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=69656bf0d7d99660e536c22472a5eae639695a97
commit 69656bf0d7d99660e536c22472a5eae639695a97
Author: Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-06-22 17:55:15 +0000
Commit: Jason W. Bacon <jwb at FreeBSD.org>
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 at 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 <bsd.port.mk>
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 <stdint.h>
+#include <sys/endian.h>
+
+/* 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 ***
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