diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile index 5ee287444dc0..c774f64a5159 100644 --- a/biology/sra-tools/Makefile +++ b/biology/sra-tools/Makefile @@ -1,67 +1,69 @@ PORTNAME= sra-tools -DISTVERSION= 3.0.6 -PORTREVISION= 1 +DISTVERSION= 3.1.1 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 LICENSE= PD LGPL21+ LICENSE_COMB= multi LICENSE_FILE_PD= ${WRKSRC}/LICENSE LICENSE_DISTFILES_LGPL21+ = -# Untested on other platforms, aarch64 support was recently added upstream ONLY_FOR_ARCHS= aarch64 amd64 ONLY_FOR_ARCHS_REASON= Upstream explicitly supports specific platforms +# hdf5 is dynamically loaded by some tools, but nothing links to it BUILD_DEPENDS= bash:shells/bash -LIB_DEPENDS= libxml2.so:textproc/libxml2 \ - libhdf5.so:science/hdf5 \ - libepoll-shim.so:devel/libepoll-shim \ - libzstd.so:archivers/zstd +RUN_DEPENDS= hdf5>0:science/hdf5 USES= bison cmake shebangfix USE_GITHUB= yes USE_LDCONFIG= ${PREFIX}/lib64 USE_JAVA= yes # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present JAVA_VERSION= 17+ OPTIONS_DEFINE= EXAMPLES SHEBANG_GLOB= *.sh GH_ACCOUNT= ncbi +# FIXME: At the time this was added, sra-tools build required access to the +# ncbi-vdb source tree. Use a separate dependent port if that is no +# longer the case. CMakeLists.txt still looks for ../ncbi-vdb in 3.1.1. GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib -post-extract: - @${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: - # 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' \ + # Reinplaces may follow static patches. Run "make clean patch" + # before updating those patches so reinplaces do not get added to them. + @${REINPLACE_CMD} -e 's|"/etc/ncbi"|"${PREFIX}/etc/ncbi"|g' \ ${WRKSRC}/ncbi-vdb/libs/kfg/config.c - ${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \ + @${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \ ${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp + @${REINPLACE_CMD} -e 's|/../ncbi-vdb|/ncbi-vdb|g' \ + ${WRKSRC}/CMakeLists.txt cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make +# FIXME: Unsure where the jquery version comes from and it differs on +# amd64 (jquery-3.7.1.min.js) and aarch64 (jquery-3.6.1.min.js). +# Just hack the version out for now. Not sure we even need javadoc installed. post-stage: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION} + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib64/*.${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 + ${MV} ${STAGEDIR}${JAVASHAREDIR}doc/ngs-doc/script-dir/jquery-[0-9]*.min.js \ + ${STAGEDIR}${JAVASHAREDIR}doc/ngs-doc/script-dir/jquery.min.js post-stage-EXAMPLES-off: ${RM} -r ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo index db2f69729c91..b69d1654ef45 100644 --- a/biology/sra-tools/distinfo +++ b/biology/sra-tools/distinfo @@ -1,5 +1,5 @@ -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 +TIMESTAMP = 1731806177 +SHA256 (ncbi-sra-tools-3.1.1_GH0.tar.gz) = 96b110bd5a30ad312e2f02552062b48a77d40c763e6aba5bb84e83662a505cf1 +SIZE (ncbi-sra-tools-3.1.1_GH0.tar.gz) = 45754110 +SHA256 (ncbi-ncbi-vdb-3.1.1_GH0.tar.gz) = e9766f259853c696be48e289b08cb5ae6e198d82d7ffee79f09ce7f720487991 +SIZE (ncbi-ncbi-vdb-3.1.1_GH0.tar.gz) = 19055901 diff --git a/biology/sra-tools/files/byteswap.h b/biology/sra-tools/files/byteswap.h deleted file mode 100644 index 807bea1289b8..000000000000 --- a/biology/sra-tools/files/byteswap.h +++ /dev/null @@ -1,15 +0,0 @@ - -#ifndef _freebsd_byteswap_h_ -#define _freebsd_byteswap_h_ - -#include - -#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 diff --git a/biology/sra-tools/files/endian.h b/biology/sra-tools/files/endian.h deleted file mode 100644 index c4b8fc49f735..000000000000 --- a/biology/sra-tools/files/endian.h +++ /dev/null @@ -1,2 +0,0 @@ - -#include diff --git a/biology/sra-tools/files/os-native.h b/biology/sra-tools/files/os-native.h deleted file mode 100644 index 7dc63e85c167..000000000000 --- a/biology/sra-tools/files/os-native.h +++ /dev/null @@ -1,43 +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. -* -* =========================================================================== -* -*/ - -#ifndef _h_os_native_ -#define _h_os_native_ - -#ifndef _h_unix_native_ -#include "../unix/unix-native.h" -#endif - -#ifdef __cplusplus -extern "C" { -#endif - - -#ifdef __cplusplus -} -#endif - -#endif /* _h_os_native_ */ diff --git a/biology/sra-tools/files/patch-CMakeLists.txt b/biology/sra-tools/files/patch-CMakeLists.txt deleted file mode 100644 index 7c864a522b85..000000000000 --- a/biology/sra-tools/files/patch-CMakeLists.txt +++ /dev/null @@ -1,13 +0,0 @@ ---- CMakeLists.txt.orig 2023-02-01 20:26:19 UTC -+++ CMakeLists.txt -@@ -54,8 +54,8 @@ set(CMAKE_MODULE_PATH - "${CMAKE_CURRENT_SOURCE_DIR}/build" - ) - --set( VDB_BINDIR "${CMAKE_BINARY_DIR}/../ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" ) --set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" ) -+set( VDB_BINDIR "${CMAKE_BINARY_DIR}/ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" ) -+set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" ) - - include(CTest) - enable_testing() diff --git a/biology/sra-tools/files/patch-build_env.cmake b/biology/sra-tools/files/patch-build_env.cmake deleted file mode 100644 index be1423fb24c2..000000000000 --- a/biology/sra-tools/files/patch-build_env.cmake +++ /dev/null @@ -1,56 +0,0 @@ ---- build/env.cmake.orig 2023-07-10 16:23:35 UTC -+++ build/env.cmake -@@ -69,11 +69,21 @@ if ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Darwin" ) - set(LIBPFX "lib") - set(SHLX "dylib") - set(STLX "a") -+elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "FreeBSD" ) -+ set(OS "bsd") -+ set(LIBPFX "lib") -+ set(SHLX "so") -+ set(STLX "a") - elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Linux" ) - set(OS "linux") - set(LIBPFX "lib") - set(SHLX "so") - set(STLX "a") -+elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "NetBSD" ) -+ set(OS "bsd") -+ set(LIBPFX "lib") -+ set(SHLX "so") -+ set(STLX "a") - elseif ( ${CMAKE_HOST_SYSTEM_NAME} STREQUAL "Windows" ) - set(OS "windows") - set(LIBPFX "") -@@ -91,6 +101,8 @@ elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "aarc - set(ARCH "arm64") - elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "x86_64") - set(ARCH "x86_64") -+elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "amd64") -+ set(ARCH "x86_64") - elseif ( ${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "AMD64") - set(ARCH "x86_64") - else() -@@ -98,7 +110,11 @@ else() - endif () - - # create variables based entirely upon OS --if ( "mac" STREQUAL ${OS} ) -+if ( "bsd" STREQUAL ${OS} ) -+ add_compile_definitions( BSD UNIX ) -+ set( LMCHECK "" ) -+ set( EXE "" ) -+elseif ( "mac" STREQUAL ${OS} ) - add_compile_definitions( MAC BSD UNIX ) - set( LMCHECK "" ) - set( EXE "" ) -@@ -380,6 +396,9 @@ endif() - - if ( "mac" STREQUAL ${OS} ) - include_directories(${VDB_INTERFACES_DIR}/os/mac) -+ include_directories(${VDB_INTERFACES_DIR}/os/unix) -+elseif( "bsd" STREQUAL ${OS} ) -+ include_directories(${VDB_INTERFACES_DIR}/os/bsd) - include_directories(${VDB_INTERFACES_DIR}/os/unix) - elseif( "linux" STREQUAL ${OS} ) - include_directories(${VDB_INTERFACES_DIR}/os/linux) diff --git a/biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt b/biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt deleted file mode 100644 index 25801b4ed932..000000000000 --- a/biology/sra-tools/files/patch-libs_ascp_CMakeLists.txt +++ /dev/null @@ -1,27 +0,0 @@ ---- libs/ascp/CMakeLists.txt.orig 2023-07-10 16:23:35 UTC -+++ libs/ascp/CMakeLists.txt -@@ -23,12 +23,17 @@ - # =========================================================================== - - set ( UNIX_SRC unix/connect.c ) -+# FIXME: Add BSD-specific ascp-path.c -+# Aspera can be installed and run with linux compat -+set ( BSD_SRC ${UNIX_SRC} linux/ascp-path.c ) - set ( LINUX_SRC ${UNIX_SRC} linux/ascp-path.c ) - set ( MAC_SRC ${UNIX_SRC} mac/ascp-path.c ) - set ( WIN_SRC win/connect.c win/ascp-path.c ) - - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "mac" STREQUAL ${OS} ) -@@ -49,4 +54,4 @@ GenerateStaticLibs(ascp - ) - - add_compile_definitions( __mod__="libs/ascp" ) --include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) -\ No newline at end of file -+include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp b/biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp deleted file mode 100644 index b16584ab8dbf..000000000000 --- a/biology/sra-tools/files/patch-libs_general-writer_general-writer.cpp +++ /dev/null @@ -1,10 +0,0 @@ ---- libs/general-writer/general-writer.cpp.orig 2023-05-11 11:57:33 UTC -+++ libs/general-writer/general-writer.cpp -@@ -39,6 +39,7 @@ - #include - - #define PROGRESS_EVENT 0 -+#define UNUSED(x) ((void)(x)) - - namespace ncbi - { diff --git a/biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake b/biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake deleted file mode 100644 index ead9978585e2..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_build_env.cmake +++ /dev/null @@ -1,47 +0,0 @@ ---- ncbi-vdb/build/env.cmake.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/build/env.cmake -@@ -75,9 +75,15 @@ set(CMAKE_CXX_EXTENSIONS OFF) - if ( ${CMAKE_SYSTEM_NAME} STREQUAL "Darwin" ) - set(OS "mac") - set(SHLX "dylib") -+elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD" ) -+ set(OS "bsd") -+ set(SHLX "so") - elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" ) - set(OS "linux") - set(SHLX "so") -+elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "NetBSD" ) -+ set(OS "bsd") -+ set(SHLX "so") - elseif ( ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" ) - set(OS "windows") - else() -@@ -99,6 +105,8 @@ elseif ( ${_system_processor} STREQUAL "x86_64") - set(ARCH "x86_64") - elseif ( ${_system_processor} STREQUAL "AMD64") - set(ARCH "x86_64") -+elseif ( ${_system_processor} STREQUAL "amd64") -+ set(ARCH "x86_64") - else () - message ( FATAL_ERROR "unknown architecture " ${_system_processor}) - endif () -@@ -110,6 +118,9 @@ if ( "mac" STREQUAL ${OS} ) - set(CMAKE_CXX_ARCHIVE_CREATE " Scr ") - set(CMAKE_C_ARCHIVE_FINISH " -no_warning_for_no_symbols -c ") - set(CMAKE_CXX_ARCHIVE_FINISH " -no_warning_for_no_symbols -c ") -+elseif( "bsd" STREQUAL ${OS} ) -+ add_compile_definitions( BSD UNIX ) -+ set( LMCHECK "" ) - elseif( "linux" STREQUAL ${OS} ) - add_compile_definitions( LINUX UNIX ) - set( LMCHECK -lmcheck ) -@@ -241,6 +252,9 @@ endif() - - if ( "mac" STREQUAL ${OS} ) - include_directories(interfaces/os/mac) -+ include_directories(interfaces/os/unix) -+elseif( "bsd" STREQUAL ${OS} ) -+ include_directories(interfaces/os/bsd) - include_directories(interfaces/os/unix) - elseif( "linux" STREQUAL ${OS} ) - include_directories(interfaces/os/linux) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp b/biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp deleted file mode 100644 index 69973928e80f..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_align_samextract-lib.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/libs/align/samextract-lib.cpp.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/align/samextract-lib.cpp -@@ -48,7 +48,7 @@ - #include - #include - --#if LINUX -+#if BSD || LINUX - #include - #define DFL_THREAD_COUNT ((int)sysconf( _SC_NPROCESSORS_ONLN ) - 1) - #else diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt deleted file mode 100644 index 4815ee9bdcbd..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_CMakeLists.txt +++ /dev/null @@ -1,19 +0,0 @@ ---- ncbi-vdb/libs/kapp/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kapp/CMakeLists.txt -@@ -23,12 +23,16 @@ - # =========================================================================== - - set ( UNIX_SRC unix/args-conv-os.c unix/sysmain.c ) -+# Must patch hw.memsize -> hw.usermem -+set ( BSD_SRC ${UNIX_SRC} mac/ram.c ) - set ( LINUX_SRC ${UNIX_SRC} linux/ram.c ) - set ( MAC_SRC ${UNIX_SRC} mac/ram.c ) - set ( WIN_SRC win/args-conv-os.c win/ram.c win/sysmain.c ) - - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "mac" STREQUAL ${OS} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c deleted file mode 100644 index 67d836a71d38..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kapp_mac_ram.c +++ /dev/null @@ -1,17 +0,0 @@ ---- ncbi-vdb/libs/kapp/mac/ram.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kapp/mac/ram.c -@@ -46,7 +46,14 @@ rc_t KAppGetTotalRam ( uint64_t * totalRam ) - - assert ( totalRam != 0 ); - -+// FIXME: This file should probably be moved to bsd/ram.c -+#if defined(__APPLE__) - ret = sysctlbyname("hw.memsize", totalRam, &len, NULL, 0 ); -+#elif defined(__FreeBSD__) || defined(__NetBSD__) -+ ret = sysctlbyname("hw.usermem", totalRam, &len, NULL, 0 ); -+#else -+ #error "You need to add a sysctl for this platform." -+#endif - if ( ret < 0 ) - { - int status = errno; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt deleted file mode 100644 index 05d204e31147..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfc_CMakeLists.txt +++ /dev/null @@ -1,25 +0,0 @@ ---- ncbi-vdb/libs/kfc/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kfc/CMakeLists.txt -@@ -23,12 +23,15 @@ - # =========================================================================== - - set ( UNIX_SRC unix/sysctx.c unix/sysrsrc.c ) -+set ( BSD_SRC ${UNIX_SRC} ) - set ( LINUX_SRC ${UNIX_SRC} ) - set ( MAC_SRC ${UNIX_SRC} ) - set ( WIN_SRC win/sysctx.c win/sysrsrc.c ) - - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "mac" STREQUAL ${OS} ) -@@ -48,4 +51,4 @@ set( SRC - GenerateStaticLibs( kfc "${SRC}" ) - - add_compile_definitions (__mod__="libs/kfc") --include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) -\ No newline at end of file -+include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c deleted file mode 100644 index 8d9268922948..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_config.c +++ /dev/null @@ -1,31 +0,0 @@ ---- ncbi-vdb/libs/kfg/config.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kfg/config.c -@@ -2574,7 +2574,7 @@ bool load_from_std_location ( KConfig *self, const KDi - const char * std_locs [] = - { - #if ! WINDOWS -- "/etc/ncbi", -+ "/usr/local/etc/ncbi", - #else - "/c/ncbi", - #endif -@@ -2588,7 +2588,7 @@ bool load_from_std_location ( KConfig *self, const KDi - NCBI_VDB_NO_ETC_NCBI_KFG[0] != '\0') - { - DBGMSG(DBG_KFG, DBG_FLAG(DBG_KFG), -- ("KFG: load from std. location /etc/ncbi is disabled. " -+ ("KFG: load from std. location /usr/local/etc/ncbi is disabled. " - "NCBI_VDB_NO_ETC_NCBI_KFG='%s'\n", NCBI_VDB_NO_ETC_NCBI_KFG)); - return loaded; - } -@@ -2839,7 +2839,9 @@ void add_predefined_nodes ( KConfig * self, const char - update_node ( self, "kfg/arch/bits", buf, true ); - - /* *OS */ --#if LINUX -+#if BSD -+ #define OS "bsd" -+#elif LINUX - #define OS "linux" - #elif MAC - #define OS "mac" diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt deleted file mode 100644 index c6b4801f527d..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_CMakeLists.txt +++ /dev/null @@ -1,35 +0,0 @@ ---- ncbi-vdb/libs/kfs/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kfs/CMakeLists.txt -@@ -23,6 +23,7 @@ - # =========================================================================== - - set ( UNIX_SRC unix/sysdir.c unix/sysdll.c unix/sysfile.c unix/syslockfile.c unix/sysmmap.c ) -+set ( BSD_SRC ${UNIX_SRC} ) - set ( LINUX_SRC ${UNIX_SRC} ) - set ( MAC_SRC ${UNIX_SRC} ) - set ( WIN_SRC win/directory-path.c win/sysdir.c win/sysdll.c win/sysfile.c win/syslockfile.c win/sysmmap.c -@@ -30,6 +31,7 @@ set ( WIN_SRC win/directory-path.c win/sysdir.c win/sy - ) - - set ( UNIX_SRC_V2 unix/sysfile-v2.c ) -+set ( BSD_SRC_V2 ${UNIX_SRC_V2} ) - set ( LINUX_SRC_V2 ${UNIX_SRC_V2} ) - set ( MAC_SRC_V2 ${UNIX_SRC_V2} ) - set ( WIN_SRC_V2 win/sysfile-v2.c ) -@@ -37,6 +39,9 @@ set ( WIN_SRC_V2 win/sysfile-v2.c ) - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) - include_directories( win ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) -+ include_directories( unix ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - include_directories( unix ) -@@ -106,4 +111,4 @@ GenerateStaticLibsWithDefs( kfs-nommap ${KFS_NOMMAP_SR - GenerateStaticLibs( kfs "${KFS_SRC}" ) - - add_compile_definitions (__mod__="libs/kfs") --include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) -\ No newline at end of file -+include_directories( BEFORE ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c deleted file mode 100644 index b128f98c29eb..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfs_unix_sysdir.c +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/libs/kfs/unix/sysdir.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kfs/unix/sysdir.c -@@ -2291,6 +2291,8 @@ rc_t KSysDirOpenDirRead_v1 ( const KSysDir_v1 * self, - rc_t rc; - - rc = KSysDirMakePath_v1 ( self, rcOpening, true, full, sizeof full, path, args ); -+ // FIXME: Remove this debug statement -+ // fprintf(stderr, "path = %s full = %s\n", path, full); - if ( rc == 0 ) - { - int t; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt deleted file mode 100644 index a854e97d5480..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_CMakeLists.txt +++ /dev/null @@ -1,18 +0,0 @@ ---- ncbi-vdb/libs/klib/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/klib/CMakeLists.txt -@@ -24,12 +24,15 @@ - - set ( UNIX_BASE_SRC unix/misc.c unix/syslog.c unix/systime.c unix/syswriter.c ) - set ( UNIX_SRC ${UNIX_BASE_SRC} unix/syserrcode.c ) -+set ( BSD_SRC ${UNIX_SRC} ) - set ( LINUX_SRC ${UNIX_BASE_SRC} linux/syserrcode.c ) - set ( MAC_SRC ${UNIX_SRC} ) - set ( WIN_SRC win/misc.c win/sysalloc.c win/syserrcode.c win/syslog.c win/systime.c win/syswriter.c ) - - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "mac" STREQUAL ${OS} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c deleted file mode 100644 index 205569c40a3e..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_hashfile.c +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi-vdb/libs/klib/hashfile.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/klib/hashfile.c -@@ -35,7 +35,7 @@ - #include - #include - #include --#if LINUX -+#if BSD || LINUX - #include - #endif - -@@ -346,7 +346,7 @@ static void * map_calloc( KHashFile * self, size_t siz - KLockUnlock( self->alloc_lock ); - return NULL; - } --#if LINUX -+#if BSD || LINUX - /* Not sure this helps */ - madvise( (void *)self->alloc_base, req, MADV_RANDOM ); - #endif diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c deleted file mode 100644 index 193f584e41fe..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_klib_unix_systime.c +++ /dev/null @@ -1,16 +0,0 @@ ---- ncbi-vdb/libs/klib/unix/systime.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/klib/unix/systime.c -@@ -142,7 +142,13 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( const KTime *sel - t . tm_isdst = self -> dst; - - ts = mktime ( &t ); -+#ifdef __FreeBSD__ -+ // This might be portable to all platforms -+ ts += localtime(&ts)->tm_gmtoff; -+#else -+ // extern global in sys/time.h on Linux and some other platforms - ts -= timezone; -+#endif - } - - return ts; diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt deleted file mode 100644 index c85b1b6631ca..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_CMakeLists.txt +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi-vdb/libs/kns/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kns/CMakeLists.txt -@@ -23,6 +23,7 @@ - # =========================================================================== - - set ( UNIX_SRC unix/sysmgr.c unix/syssock.c unix/sysstream.c ) -+set ( BSD_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c ) - set ( LINUX_SRC ${UNIX_SRC} linux/sysendpoint.c linux/syspoll.c ) - set ( MAC_SRC ${UNIX_SRC} mac/sysendpoint.c mac/syspoll.c ) - set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/syssock.c win/sysstream.c ) -@@ -30,6 +31,9 @@ set ( WIN_SRC win/sysendpoint.c win/sysmgr.c win/sysso - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) - include_directories( win ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) -+ include_directories( unix ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - include_directories( unix ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c deleted file mode 100644 index 816454bea102..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_manager.c +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/libs/kns/manager.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kns/manager.c -@@ -58,7 +58,7 @@ - #if HAVE_GNU_LIBC_VERSION_H - #include - #endif --#if LINUX -+#if BSD || LINUX - #include - #include - #endif diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c b/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c deleted file mode 100644 index 313461f90846..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kns_unix_syssock.c +++ /dev/null @@ -1,10 +0,0 @@ ---- ncbi-vdb/libs/kns/unix/syssock.c.orig 2023-08-07 20:34:54 UTC -+++ ncbi-vdb/libs/kns/unix/syssock.c -@@ -66,6 +66,7 @@ - #include - #include - #include -+#include - #include - #include - #include diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt deleted file mode 100644 index 2f4e808e2d65..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_kproc_CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ ---- ncbi-vdb/libs/kproc/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/kproc/CMakeLists.txt -@@ -23,6 +23,7 @@ - # =========================================================================== - - set ( UNIX_SRC unix/syscond.c unix/systhread.c unix/systimeout.c ) -+set ( BSD_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c) - set ( LINUX_SRC ${UNIX_SRC} linux/sysbarrier.c linux/syslock.c linux/sysmgr.c ) - set ( MAC_SRC ${UNIX_SRC} bsd/syslock.c bsd/sysmgr.c) - set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c win/systhread.c win/systimeout.c ) -@@ -30,6 +31,10 @@ set ( WIN_SRC win/syscond.c win/syslock.c win/sysmgr.c - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) - include_directories( win ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) -+ include_directories( bsd ) -+ include_directories( unix ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - include_directories( linux ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt deleted file mode 100644 index 78926849f124..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_ktst_CMakeLists.txt +++ /dev/null @@ -1,18 +0,0 @@ ---- ncbi-vdb/libs/ktst/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/ktst/CMakeLists.txt -@@ -23,12 +23,15 @@ - # =========================================================================== - - set ( UNIX_SRC unix/systestenv ) -+set ( BSD_SRC ${UNIX_SRC} ) - set ( LINUX_SRC ${UNIX_SRC} ) - set ( MAC_SRC ${UNIX_SRC} ) - set ( WIN_SRC win/systestenv ) - - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "mac" STREQUAL ${OS} ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt deleted file mode 100644 index 5d670acdbe4b..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_libs_vfs_CMakeLists.txt +++ /dev/null @@ -1,25 +0,0 @@ ---- ncbi-vdb/libs/vfs/CMakeLists.txt.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/libs/vfs/CMakeLists.txt -@@ -23,12 +23,15 @@ - # =========================================================================== - - set ( UNIX_SRC unix/syskeyring.c unix/syspath.c ) -+set ( BSD_SRC ${UNIX_SRC} ) - set ( LINUX_SRC ${UNIX_SRC} ) - set ( MAC_SRC ${UNIX_SRC} ) - set ( WIN_SRC win/syskeyring.c win/syspath.c ) - - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - elseif( "mac" STREQUAL ${OS} ) -@@ -54,4 +57,4 @@ set( SRC - GenerateStaticLibs( vfs "${SRC}" ) - - add_compile_definitions (__mod__="libs/vfs") --include_directories(${CMAKE_CURRENT_SOURCE_DIR}) -\ No newline at end of file -+include_directories(${CMAKE_CURRENT_SOURCE_DIR}) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kapp_run-sig-core.sh b/biology/sra-tools/files/patch-ncbi-vdb_test_kapp_run-sig-core.sh deleted file mode 100644 index ebc81bd3fc5b..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_kapp_run-sig-core.sh +++ /dev/null @@ -1,49 +0,0 @@ ---- ncbi-vdb/test/kapp/run-sig-core.sh.orig 2017-10-27 07:23:08 UTC -+++ ncbi-vdb/test/kapp/run-sig-core.sh -@@ -29,12 +29,12 @@ BUILD_TYPE="$3" - - SIGQUIT=3 - --function killFromBackground () -+killFromBackground () - { - PARENT_PID=$1 - for I in 1 2 3 4 5 - do -- COMMAND="ps -ef|awk '\$3==${PARENT_PID} && \$8==\"${BINARY_PATH}\" {print \$2}'" -+ COMMAND="ps awwo pid,ppid,command|awk '\$2==${PARENT_PID} && \$3==\"${BINARY_PATH}\" {print \$1}'" - eval PID=\`${COMMAND}\` - if [ "$PID" = "" ]; then - sleep 1 -@@ -44,7 +44,7 @@ function killFromBackground () - done - - if [ "$PID" != "" ]; then -- kill -s $SIGQUIT $PID -+ kill -s QUIT $PID - fi - - echo $PID > killed.pid -@@ -63,6 +63,13 @@ if [ "$HOST_OS" = "mac" ]; then - fi - - CORE_FOLDER="/core/" -+elif [ "$HOST_OS" = "bsd" ]; then -+ if [ "`ulimit -c`" = "0" ] || [ "`/sbin/sysctl -n kern.coredump`" != "1" ]; then -+ echo "Core files are disabled. Skipping core file tests" -+ exit 0 -+ fi -+ -+ CORE_FOLDER="./" - elif [ "$HOST_OS" = "linux" ]; then - if [ "`ulimit -c`" = "0" ]; then - echo "Core files are disabled. Skipping core file tests" -@@ -92,7 +99,7 @@ wait - BINARY_PID=`cat killed.pid` - rm killed.pid - --CORE_FILE="${CORE_FOLDER}core.${BINARY_PID}" -+CORE_FILE="${CORE_FOLDER}${BINARY_PATH##*/}.core" - - if [ "$BUILD_TYPE" = "dbg" ]; then - if [ -f $CORE_FILE ]; then diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp deleted file mode 100644 index ce1bb1b02508..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_kfg_kfgtest.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/test/kfg/kfgtest.cpp.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/test/kfg/kfgtest.cpp -@@ -282,6 +282,8 @@ FIXTURE_TEST_CASE(predef_ARCHBITS, KfgFixture) - FIXTURE_TEST_CASE(predef_OS, KfgFixture) - { - CreateAndLoad(GetName(), "var=$(OS)\n"); -+ #if BSD -+ #define OS "bsd" - #if LINUX - #define OS "linux" - #elif SUN diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c b/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c deleted file mode 100644 index 0ce58974e6ed..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_klib_printf-test.c +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi-vdb/test/klib/printf-test.c.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/test/klib/printf-test.c -@@ -504,7 +504,7 @@ rc_t run ( const char *progname ) - if ( rc == 0 ) - { - rc = make_initial_test ( field_width, precision, " ", "s", "Kurt is having a fit" ); --#if !defined(__SunOS) && !defined(__sun__) -+#if !defined(__SunOS) && !defined(__sun__) && !defined(__FreeBSD__) - /* Solaris printf doesn't cope with NULLs */ - #if 0 - /* The standard says this result is undefined, we shouldn't test for it, it is not consistent */ diff --git a/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp b/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp deleted file mode 100644 index b063ef020502..000000000000 --- a/biology/sra-tools/files/patch-ncbi-vdb_test_vdb_test-dependencies__dflt.cpp +++ /dev/null @@ -1,12 +0,0 @@ ---- ncbi-vdb/test/vdb/test-dependencies_dflt.cpp.orig 2023-07-10 16:13:36 UTC -+++ ncbi-vdb/test/vdb/test-dependencies_dflt.cpp -@@ -139,6 +139,9 @@ class EmptyFixture : public DepFixture { (public) - - class RefseqFixture : public DepFixture { - -+ #if BSD -+ // FIXME: Should there be a separate kfg/freebsd? -+ #define PATH "kfg/linux" - #if LINUX - #define PATH "kfg/linux" - #elif MAC diff --git a/biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp b/biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp deleted file mode 100644 index 9c995dcdbc51..000000000000 --- a/biology/sra-tools/files/patch-tools_external_driver-tool_file-path.posix.cpp +++ /dev/null @@ -1,20 +0,0 @@ ---- tools/external/driver-tool/file-path.posix.cpp.orig 2023-07-10 16:23:35 UTC -+++ tools/external/driver-tool/file-path.posix.cpp -@@ -193,7 +193,16 @@ static char const *find_executable_path(char const *co - FilePath FilePath::fullPathToExecutable(char const *const *const argv, char const *const *const envp, char const *const *const extra) - { - char const *path; --#if LINUX -+// Assume sra-tools is installed by FreeBSD ports. FreeBSD users -+// don't often install software by other means. Default prefix -+// is /usr/local, but this can be overridden by the user building -+// the port. The port can replace /usr/local using sed if that's the -+// case. -+#if BSD -+ char full_path[PATH_MAX]; -+ snprintf(full_path, PATH_MAX, "/usr/local/bin/%s", argv[0]); -+ path = full_path; -+#elif LINUX - path = "/proc/self/exe"; - #elif MAC - path = find_executable_path(extra, argv[0]); diff --git a/biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp b/biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp deleted file mode 100644 index bea51c07e42e..000000000000 --- a/biology/sra-tools/files/patch-tools_external_driver-tool_sratools.cpp +++ /dev/null @@ -1,25 +0,0 @@ ---- tools/external/driver-tool/sratools.cpp.orig 2023-07-10 16:23:35 UTC -+++ tools/external/driver-tool/sratools.cpp -@@ -420,6 +420,7 @@ static int main(CommandLine const &argv) - enableLogging(argv.toolName.c_str()); - #endif - LOG(7) << "executable path: " << (std::string)argv.fullPathToExe << std::endl; -+ // std::cerr << "executable path: " << (std::string)argv.fullPathToExe << std::endl; - - config = new Config(); - struct Defer { ~Defer() { delete config; config = nullptr; } } freeConfig; -@@ -576,6 +577,14 @@ static int main(CommandLine const &argv) - } - - } // namespace sratools -+ -+#if BSD -+int main(int argc, char *argv[], char *envp[]) -+{ -+ auto const invocation = CommandLine(argc, argv, envp, nullptr); -+ return sratools::main(invocation); -+} -+#endif - - #if MAC - int main(int argc, char *argv[], char *envp[], char *apple[]) diff --git a/biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt b/biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt deleted file mode 100644 index d3627cbbc42a..000000000000 --- a/biology/sra-tools/files/patch-tools_external_vdb-config_tui_CMakeLists.txt +++ /dev/null @@ -1,20 +0,0 @@ ---- tools/external/vdb-config/tui/CMakeLists.txt.orig 2023-07-10 16:23:35 UTC -+++ tools/external/vdb-config/tui/CMakeLists.txt -@@ -25,6 +25,7 @@ - include_directories( ${CMAKE_CURRENT_SOURCE_DIR}/.. ) - - set ( UNIX_SRC unix/systui.c ) -+set ( BSD_SRC bsd/systui.c ) - set ( LINUX_SRC linux/systui.c ) - set ( MAC_SRC bsd/systui.c ) - set ( WIN_SRC win/systui.c ) -@@ -32,6 +33,9 @@ set ( WIN_SRC win/systui.c ) - if ( "windows" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${WIN_SRC} ) - #include_directories( win ) -+elseif( "bsd" STREQUAL ${OS} ) -+ set ( OS_SPECIFIC_SRC ${BSD_SRC} ) -+ #include_directories( unix ) - elseif( "linux" STREQUAL ${OS} ) - set ( OS_SPECIFIC_SRC ${LINUX_SRC} ) - #include_directories( unix ) diff --git a/biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c b/biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c deleted file mode 100644 index 2b337b2116e5..000000000000 --- a/biology/sra-tools/files/patch-tools_loaders_fastq-loader_spot-assembler.c +++ /dev/null @@ -1,17 +0,0 @@ ---- tools/loaders/fastq-loader/spot-assembler.c.orig 2023-08-08 12:26:35 UTC -+++ tools/loaders/fastq-loader/spot-assembler.c -@@ -1,3 +1,4 @@ -+ - /*=========================================================================== - * - * PUBLIC DOMAIN NOTICE -@@ -25,6 +26,9 @@ - */ - - #include "spot-assembler.h" -+ -+// FIXME: Unsure if this is still necessary -+#include - - #include - #include diff --git a/biology/sra-tools/pkg-descr b/biology/sra-tools/pkg-descr index 06ed34546192..40b82b646dc0 100644 --- a/biology/sra-tools/pkg-descr +++ b/biology/sra-tools/pkg-descr @@ -1,13 +1,7 @@ -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. -SRA tools allows conversion of .sra files, which INSDC SRAs maintain, -from/to other formats that the 'next-gen' sequenecers generate including: -* csfasta/csqual (ABI SOLiD) -* fastq (and fasta for writing) -* hdf5 (PacBio, reading only) -* qseq (older Illumina) -* sam (writing only) / bam (reading only) -* sff -The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data -and local SRA files. +The SRA Toolkit and SDK from NCBI is a collection of tools and +libraries for using data in the INSDC (International Nucleotide +Sequence Database Collaboration) SRA (Sequence Read Archives). The +SRA house sequence reads and alignments generated by DNA/RNA +sequencers. The SRA Toolkit facilitates downloading sequence data, +performing filtering and conversions on-the-fly, thus saving enormous +amounts of time, bandwidth, and storage. diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist index 1976fb428463..f4ac6a2b7d44 100644 --- a/biology/sra-tools/pkg-plist +++ b/biology/sra-tools/pkg-plist @@ -1,282 +1,282 @@ bin/abi-dump bin/abi-dump.3 -bin/abi-dump.3.0.6 +bin/abi-dump.3.1.1 bin/align-info bin/align-info.3 -bin/align-info.3.0.6 +bin/align-info.3.1.1 bin/cache-mgr bin/cache-mgr.3 -bin/cache-mgr.3.0.6 +bin/cache-mgr.3.1.1 bin/check-corrupt bin/check-corrupt.3 -bin/check-corrupt.3.0.6 +bin/check-corrupt.3.1.1 bin/fasterq-dump -bin/fasterq-dump-orig.3.0.6 +bin/fasterq-dump-orig.3.1.1 bin/fasterq-dump.3 -bin/fasterq-dump.3.0.6 +bin/fasterq-dump.3.1.1 bin/fastq-dump -bin/fastq-dump-orig.3.0.6 +bin/fastq-dump-orig.3.1.1 bin/fastq-dump.3 -bin/fastq-dump.3.0.6 +bin/fastq-dump.3.1.1 bin/illumina-dump bin/illumina-dump.3 -bin/illumina-dump.3.0.6 +bin/illumina-dump.3.1.1 bin/kdbmeta bin/kdbmeta.3 -bin/kdbmeta.3.0.6 +bin/kdbmeta.3.1.1 bin/ngs-pileup bin/ngs-pileup.3 -bin/ngs-pileup.3.0.6 +bin/ngs-pileup.3.1.1 bin/prefetch -bin/prefetch-orig.3.0.6 +bin/prefetch-orig.3.1.1 bin/prefetch.3 -bin/prefetch.3.0.6 +bin/prefetch.3.1.1 bin/rcexplain bin/rcexplain.3 -bin/rcexplain.3.0.6 +bin/rcexplain.3.1.1 bin/ref-variation bin/ref-variation.3 -bin/ref-variation.3.0.6 +bin/ref-variation.3.1.1 bin/sam-dump -bin/sam-dump-orig.3.0.6 +bin/sam-dump-orig.3.1.1 bin/sam-dump.3 -bin/sam-dump.3.0.6 +bin/sam-dump.3.1.1 bin/sff-dump bin/sff-dump.3 -bin/sff-dump.3.0.6 +bin/sff-dump.3.1.1 bin/sra-info bin/sra-info.3 -bin/sra-info.3.0.6 +bin/sra-info.3.1.1 bin/sra-pileup -bin/sra-pileup-orig.3.0.6 +bin/sra-pileup-orig.3.1.1 bin/sra-pileup.3 -bin/sra-pileup.3.0.6 +bin/sra-pileup.3.1.1 bin/sra-search bin/sra-search.3 -bin/sra-search.3.0.6 +bin/sra-search.3.1.1 bin/sra-stat bin/sra-stat.3 -bin/sra-stat.3.0.6 +bin/sra-stat.3.1.1 bin/srapath -bin/srapath-orig.3.0.6 +bin/srapath-orig.3.1.1 bin/srapath.3 -bin/srapath.3.0.6 +bin/srapath.3.1.1 bin/sratools bin/sratools.3 -bin/sratools.3.0.6 +bin/sratools.3.1.1 bin/test-sra bin/test-sra.3 -bin/test-sra.3.0.6 +bin/test-sra.3.1.1 bin/var-expand bin/var-expand.3 -bin/var-expand.3.0.6 +bin/var-expand.3.1.1 bin/vdb-config bin/vdb-config.3 -bin/vdb-config.3.0.6 +bin/vdb-config.3.1.1 bin/vdb-decrypt bin/vdb-decrypt.3 -bin/vdb-decrypt.3.0.6 +bin/vdb-decrypt.3.1.1 bin/vdb-dump -bin/vdb-dump-orig.3.0.6 +bin/vdb-dump-orig.3.1.1 bin/vdb-dump.3 -bin/vdb-dump.3.0.6 +bin/vdb-dump.3.1.1 bin/vdb-encrypt bin/vdb-encrypt.3 -bin/vdb-encrypt.3.0.6 +bin/vdb-encrypt.3.1.1 bin/vdb-validate bin/vdb-validate.3 -bin/vdb-validate.3.0.6 +bin/vdb-validate.3.1.1 include/ncbi-vdb/NGS.hpp include/ngs/Alignment.hpp include/ngs/AlignmentIterator.hpp include/ngs/ErrorMsg.hpp include/ngs/Fragment.hpp include/ngs/FragmentIterator.hpp include/ngs/Package.hpp include/ngs/Pileup.hpp include/ngs/PileupEvent.hpp include/ngs/PileupEventIterator.hpp include/ngs/PileupIterator.hpp include/ngs/Read.hpp include/ngs/ReadCollection.hpp include/ngs/ReadGroup.hpp include/ngs/ReadGroupIterator.hpp include/ngs/ReadIterator.hpp include/ngs/Reference.hpp include/ngs/ReferenceIterator.hpp include/ngs/ReferenceSequence.hpp include/ngs/Statistics.hpp include/ngs/StringRef.hpp include/ngs/adapter/AlignmentItf.hpp include/ngs/adapter/ErrorMsg.hpp include/ngs/adapter/FragmentItf.hpp include/ngs/adapter/PileupEventItf.hpp include/ngs/adapter/PileupItf.hpp include/ngs/adapter/ReadCollectionItf.hpp include/ngs/adapter/ReadGroupItf.hpp include/ngs/adapter/ReadItf.hpp include/ngs/adapter/Refcount.hpp include/ngs/adapter/ReferenceItf.hpp include/ngs/adapter/ReferenceSequenceItf.hpp include/ngs/adapter/StatisticsItf.hpp include/ngs/adapter/StringItf.hpp include/ngs/adapter/defs.h include/ngs/inl/Alignment.hpp include/ngs/inl/AlignmentIterator.hpp include/ngs/inl/Fragment.hpp include/ngs/inl/FragmentIterator.hpp include/ngs/inl/Package.hpp include/ngs/inl/Pileup.hpp include/ngs/inl/PileupEvent.hpp include/ngs/inl/PileupEventIterator.hpp include/ngs/inl/PileupIterator.hpp include/ngs/inl/Read.hpp include/ngs/inl/ReadCollection.hpp include/ngs/inl/ReadGroup.hpp include/ngs/inl/ReadGroupIterator.hpp include/ngs/inl/ReadIterator.hpp include/ngs/inl/Reference.hpp include/ngs/inl/ReferenceIterator.hpp include/ngs/inl/ReferenceSequence.hpp include/ngs/inl/Statistics.hpp include/ngs/inl/StringRef.hpp include/ngs/itf/AlignmentItf.h include/ngs/itf/AlignmentItf.hpp include/ngs/itf/ErrBlock.h include/ngs/itf/ErrBlock.hpp include/ngs/itf/ErrorMsg.hpp include/ngs/itf/FragmentItf.h include/ngs/itf/FragmentItf.hpp include/ngs/itf/PackageItf.hpp include/ngs/itf/PileupEventItf.h include/ngs/itf/PileupEventItf.hpp include/ngs/itf/PileupItf.h include/ngs/itf/PileupItf.hpp include/ngs/itf/ReadCollectionItf.h include/ngs/itf/ReadCollectionItf.hpp include/ngs/itf/ReadGroupItf.h 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