git: 0f2f80ca3833 - main - biology/sra-tools: Update to 3.0.6
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Date: Thu, 10 Aug 2023 17:20:36 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=0f2f80ca3833a64ea2d60aa706cf794d5e0ffd63
commit 0f2f80ca3833a64ea2d60aa706cf794d5e0ffd63
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-08-10 17:17:24 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-08-10 17:17:24 +0000
biology/sra-tools: Update to 3.0.6
Major code and build system rework since 2.11
Now supports aarch64, unblocking rna-seq and atac-seq metaports
Changes: https://github.com/ncbi/sra-tools/commits/master
Reported by: portscout
---
biology/sra-tools/Makefile | 128 +++-----
biology/sra-tools/distinfo | 12 +-
biology/sra-tools/files/Makefile.bsd | 72 -----
biology/sra-tools/files/byteswap.h | 37 +--
biology/sra-tools/files/endian.h | 2 +
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 ---------
biology/sra-tools/files/os-native.h | 43 +++
biology/sra-tools/files/patch-CMakeLists.txt | 13 +
biology/sra-tools/files/patch-build_env.cmake | 56 ++++
.../sra-tools/files/patch-build_ld.linux.exe.sh | 11 -
biology/sra-tools/files/patch-hdf5 | 30 --
.../sra-tools/files/patch-libs_ascp_CMakeLists.txt | 27 ++
.../patch-libs_general-writer_general-writer.cpp | 10 +
.../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 --
.../sra-tools/files/patch-ncbi-vdb_build_env.cmake | 47 +++
.../patch-ncbi-vdb_interfaces_os_sun_atomic32.h | 85 ------
.../patch-ncbi-vdb_libs_align_samextract-lib.cpp | 11 +
.../files/patch-ncbi-vdb_libs_ext_Makefile | 12 -
.../files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt | 19 ++
.../files/patch-ncbi-vdb_libs_kapp_mac_ram.c | 17 ++
.../files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt | 25 ++
.../files/patch-ncbi-vdb_libs_kfg_config.c | 33 ++-
.../files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt | 35 +++
.../files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c | 11 +
.../files/patch-ncbi-vdb_libs_klib_CMakeLists.txt | 18 ++
.../files/patch-ncbi-vdb_libs_klib_hashfile.c | 20 ++
.../files/patch-ncbi-vdb_libs_klib_unix_systime.c | 13 +-
.../files/patch-ncbi-vdb_libs_kns_CMakeLists.txt | 20 ++
.../files/patch-ncbi-vdb_libs_kns_manager.c | 11 +
.../files/patch-ncbi-vdb_libs_kns_unix_syssock.c | 2 +-
.../files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt | 21 ++
.../files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt | 18 ++
.../files/patch-ncbi-vdb_libs_ncbi-vdb_Makefile | 20 --
.../files/patch-ncbi-vdb_libs_search_Makefile | 12 -
.../files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt | 25 ++
.../files/patch-ncbi-vdb_setup_konfigure.perl | 243 ---------------
.../files/patch-ncbi-vdb_setup_os-arch.prl | 20 --
.../files/patch-ncbi-vdb_test_kfg_kfgtest.cpp | 12 +-
.../files/patch-ncbi-vdb_test_klib_printf-test.c | 8 +-
.../files/patch-ncbi-vdb_test_kns_Makefile | 19 --
.../patch-ncbi-vdb_test_vdb_test-dependencies.cpp | 11 -
...h-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp | 12 +
...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 -
...-tools_external_driver-tool_file-path.posix.cpp | 20 ++
.../patch-tools_external_driver-tool_sratools.cpp | 25 ++
...ch-tools_external_vdb-config_tui_CMakeLists.txt | 20 ++
.../patch-tools_fastq-loader_spot-assembler.c | 11 -
...tch-tools_loaders_fastq-loader_spot-assembler.c | 17 ++
.../sra-tools/files/patch-tools_sra-sort_Makefile | 13 -
.../files/patch-tools_util_validate-names4.c | 13 -
biology/sra-tools/pkg-descr | 3 -
biology/sra-tools/pkg-plist | 293 +++++++++++++++---
69 files changed, 898 insertions(+), 2226 deletions(-)
diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index b7a0da7240bf..39dd02760918 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -1,109 +1,67 @@
PORTNAME= sra-tools
-DISTVERSION= 2.11.0
-PORTREVISION= 4
-CATEGORIES= biology
+DISTVERSION= 3.0.6
+CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org
COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives
-WWW= https://github.com/ncbi/sra-tools/wiki
+WWW= https://github.com/ncbi/sra-tools
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
+# Untested on other platforms, aarch64 support was recently added upstream
+ONLY_FOR_ARCHS= aarch64 amd64
+ONLY_FOR_ARCHS_REASON= Upstream explicitly supports specific platforms
-BUILD_DEPENDS= bash:shells/bash \
- ${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
+BUILD_DEPENDS= bash:shells/bash
LIB_DEPENDS= libxml2.so:textproc/libxml2 \
libhdf5.so:science/hdf5 \
- libepoll-shim.so:devel/libepoll-shim
+ libepoll-shim.so:devel/libepoll-shim \
+ libzstd.so:archivers/zstd
-USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix
-USE_PERL5= build
+USES= bison cmake shebangfix
USE_GITHUB= yes
+USE_LDCONFIG= ${PREFIX}/lib64
+USE_JAVA= yes
-SHEBANG_GLOB= *.sh *.pl
-GH_ACCOUNT= ncbi
-GH_TUPLE+= ncbi:ngs:${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$$(${FREEBSD_RELEASE})
-MAKE_ARGS= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
- INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
-
-NCBI_VDB_WRKSRC= ${WRKSRC}/ncbi-vdb
-NCBI_VDB_FILESDIR= ${FILESDIR}
-FREEBSD_RELEASE= uname -r | cut -d - -f 1
-
-CFLAGS+= -I${WRKSRC}/interfaces/os/sun
-CXXFLAGS+= -I${WRKSRC}/interfaces/os/sun
-
-CONFLICTS_INSTALL= kget
+# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
+JAVA_VERSION= 17+
-BINARY_ALIAS= gcc=${CC} g++=${CXX}
+OPTIONS_DEFINE= EXAMPLES
-# for port developers, building with these options may fail
-OPTIONS_DEFINE= DEBUG OPTIMIZED_CFLAGS TEST
-DEBUG_PREVENTS= OPTIMIZED_CFLAGS
-DEBUG_CONFIGURE_WITH= debug
-OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT=""
-TEST_TEST_TARGET= test
-TEST_USES= python
-
-# ncbi-vdb build extras
-VDB_CONFIGURE_ARGS= \
- --with-xml2-prefix=${LOCALBASE} \
- --with-hdf5-prefix=${LOCALBASE} \
- --prefix=${PREFIX} \
- --build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \
- CC="${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 \
- ${NCBI_VDB_WRKSRC}/interfaces/os/bsd/
+SHEBANG_GLOB= *.sh
+GH_ACCOUNT= ncbi
+GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
-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 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64
+WITH_DEBUG= yes
+CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
-post-patch-TEST-on:
- @${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile
+post-extract:
+ @${MKDIR} ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
+ @${CP} ${FILESDIR}/*.h ${WRKSRC}/ncbi-vdb/interfaces/os/bsd
+ # cd ${WRKDIR} && ${LN} -s ${WRKSRC}/ncbi-vdb .
pre-configure:
- @${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
+ # This follows a static patch. Run "make clean patch" before
+ # updating the patch.
+ ${REINPLACE_CMD} -e 's|/usr/local/etc/ncbi|${PREFIX}/etc/ncbi|g' \
+ ${WRKSRC}/ncbi-vdb/libs/kfg/config.c
+ ${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
+ ${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
+ cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
+
+post-stage:
+ ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
+ ${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools
+ ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+ ${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR}
+ ${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools
+ ${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java
+ ${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python
+
+post-stage-EXAMPLES-off:
+ ${RM} -r ${STAGEDIR}${EXAMPLESDIR}
.include <bsd.port.mk>
diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo
index fa75acf23fe6..db2f69729c91 100644
--- a/biology/sra-tools/distinfo
+++ b/biology/sra-tools/distinfo
@@ -1,7 +1,5 @@
-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
+TIMESTAMP = 1691599515
+SHA256 (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 9fecfd819ee9beaf8a1d3e4b76a5d49e747bc064525b40416e0730a168986348
+SIZE (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 44957431
+SHA256 (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 4b6f93336bf8664fdcc151d41ea0793f0b0f88cfcb7c2aa049f162a72f905223
+SIZE (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 18972238
diff --git a/biology/sra-tools/files/Makefile.bsd b/biology/sra-tools/files/Makefile.bsd
deleted file mode 100644
index 7692ec277948..000000000000
--- a/biology/sra-tools/files/Makefile.bsd
+++ /dev/null
@@ -1,72 +0,0 @@
-# ===========================================================================
-#
-# 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
index ef07fe98db64..807bea1289b8 100644
--- a/biology/sra-tools/files/byteswap.h
+++ b/biology/sra-tools/files/byteswap.h
@@ -1,40 +1,15 @@
-/*===========================================================================
-*
-* 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_
+#ifndef _freebsd_byteswap_h_
+#define _freebsd_byteswap_h_
-#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 __BYTE_ORDER _BYTE_ORDER
+#define __BIG_ENDIAN _BIG_ENDIAN
+#define __LITTLE_ENDIAN _LITTLE_ENDIAN
#define bswap_16(x) bswap16 (x)
#define bswap_32(x) bswap32 (x)
#define bswap_64(x) bswap64 (x)
-#endif /* _h_byteswap_ */
+#endif
diff --git a/biology/sra-tools/files/endian.h b/biology/sra-tools/files/endian.h
new file mode 100644
index 000000000000..c4b8fc49f735
--- /dev/null
+++ b/biology/sra-tools/files/endian.h
@@ -0,0 +1,2 @@
+
+#include <sys/endian.h>
diff --git a/biology/sra-tools/files/ld.bsd.clang.sh b/biology/sra-tools/files/ld.bsd.clang.sh
deleted file mode 100755
index 61c7779adcf1..000000000000
--- a/biology/sra-tools/files/ld.bsd.clang.sh
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/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
deleted file mode 100755
index a0a65f39884b..000000000000
--- a/biology/sra-tools/files/ld.bsd.cmn.sh
+++ /dev/null
@@ -1,158 +0,0 @@
-#!/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 $LD_REF_SYMBOLS"
- LD_ALL_STATE=0
- fi
-}
diff --git a/biology/sra-tools/files/ld.bsd.dlib.sh b/biology/sra-tools/files/ld.bsd.dlib.sh
deleted file mode 100755
index a74f2b006818..000000000000
--- a/biology/sra-tools/files/ld.bsd.dlib.sh
+++ /dev/null
@@ -1,308 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-# PUBLIC DOMAIN NOTICE
-# National Center for Biotechnology Information
-#
-# This software/database is a "United States Government Work" under the
-# terms of the United States Copyright Act. It was written as part of
-# the author's official duties as a United States Government employee and
-# thus cannot be copyrighted. This software/database is freely available
-# to the public for use. The National Library of Medicine and the U.S.
-# Government have not placed any restriction on its use or reproduction.
-#
-# Although all reasonable efforts have been taken to ensure the accuracy
-# and reliability of the software and data, the NLM and the U.S.
-# Government do not and cannot warrant the performance or results that
-# may be obtained by using this software or data. The NLM and the U.S.
-# Government disclaim all warranties, express or implied, including
-# warranties of performance, merchantability or fitness for any particular
-# purpose.
-#
-# Please cite the author in any work or product based on this material.
-#
-# ===========================================================================
-
-
-# ===========================================================================
-# input library types, and their handling
-#
-# normal linkage
-# -l : find shared or static
-# -s : require static
-# -d : require shared
-#
-# static linkage
-# -l : require static
-# -s : require static
-# -d : ignore
-# ===========================================================================
-
-
-# script name
-SELF_NAME="$(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 > "$TARG.md5"
-fi
diff --git a/biology/sra-tools/files/ld.bsd.exe.sh b/biology/sra-tools/files/ld.bsd.exe.sh
deleted file mode 100755
index 650a212780c3..000000000000
--- a/biology/sra-tools/files/ld.bsd.exe.sh
+++ /dev/null
@@ -1,326 +0,0 @@
-#!/usr/local/bin/bash
-# ===========================================================================
-#
-# PUBLIC DOMAIN NOTICE
-# National Center for Biotechnology Information
-#
-# This software/database is a "United States Government Work" under the
-# terms of the United States Copyright Act. It was written as part of
-# the author's official duties as a United States Government employee and
-# thus cannot be copyrighted. This software/database is freely available
-# to the public for use. The National Library of Medicine and the U.S.
-# Government have not placed any restriction on its use or reproduction.
-#
-# Although all reasonable efforts have been taken to ensure the accuracy
-# and reliability of the software and data, the NLM and the U.S.
-# Government do not and cannot warrant the performance or results that
-# may be obtained by using this software or data. The NLM and the U.S.
-# Government disclaim all warranties, express or implied, including
-# warranties of performance, merchantability or fitness for any particular
-# purpose.
-#
-# Please cite the author in any work or product based on this material.
-#
-# ===========================================================================
-
-
-# ===========================================================================
-# input library types, and their handling
-#
-# normal linkage
-# -l : find shared or static
-# -s : require static
-# -d : ignore - will be dynamically loaded
-#
-# static linkage
-# -l : require static
-# -s : require static
-# -d : require static
-# ===========================================================================
-
-
-# script name
-SELF_NAME="$(basename $0)"
-BUILD_DIR="$(dirname $0)"
-
-# parameters and common functions
-source "${0%exe.sh}cmn.sh"
-
-# discover tool chain
*** 2731 LINES SKIPPED ***