Index: biology/sra-tools/Makefile =================================================================== --- biology/sra-tools/Makefile (nonexistent) +++ biology/sra-tools/Makefile (working copy) @@ -0,0 +1,69 @@ +# $FreeBSD$ + +PORTNAME= sra-tools +DISTVERSION= 2.8.2-3 +CATEGORIES= biology + +MAINTAINER= mzaki@niid.go.jp +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+ = +# The executables contain functions from biology/ncbi-vdb port, +# which is derived from a part of LGPL-licensed GNU C Library or Judy library. + +BUILD_DEPENDS= bash:shells/bash \ + ${NONEXISTENT}:biology/ncbi-vdb:build \ + ${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk +LIB_DEPENDS= libxml2.so:textproc/libxml2 \ + libhdf5.so:science/hdf5 \ + libmbedtls.so:security/mbedtls + +USE_GITHUB= yes +GH_ACCOUNT= ncbi + +USES= compiler gmake perl5 shebangfix +USE_PERL5= build +SHEBANG_GLOB= *.sh *.pl + +GNU_CONFIGURE= yes +VDBSRC_CMD= ${MAKE} -C ${.CURDIR}/../ncbi-vdb -V WRKSRC +CONFIGURE_ARGS= --with-ngs-sdk-prefix=${LOCALBASE} \ + --with-ncbi-vdb-sources=$$(${VDBSRC_CMD}) \ + --with-ncbi-vdb-build=$$(${VDBSRC_CMD})/${CONFIGURE_TARGET}/ncbi-vdb/ \ + --with-xml2-prefix=${LOCALBASE} \ + --with-hdf5-prefix=${LOCALBASE} \ + --with-mbedtls-prefix=${LOCALBASE} \ + CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" +MAKE_ARGS= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \ + INST_ETCDIR=${STAGEDIR}${PREFIX}/etc + +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= NCBI-VDB requires SSE2 instructions +BROKEN_i386= buggy output + +# for port developpers, building with these options may fail +OPTIONS_DEFINE= DEBUG GCC OPTIMIZED_CFLAGS TEST +DEBUG_PREVENTS= OPTIMIZED_CFLAGS +DEBUG_CONFIGURE_WITH= debug +GCC_USE= gcc=yes +OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT="" +TEST_TEST_TARGET= test +TEST_USES= python + +pre-patch: + @${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/ + @for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done + @${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh + +post-patch-TEST-on: + ${REINPLACE_CMD} -e 's#python#${PYTHON_CMD}#' ${WRKSRC}/test/kget/Makefile + +post-configure: + @${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP + +post-build-TEST-on: do-test + +.include Property changes on: biology/sra-tools/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/distinfo =================================================================== --- biology/sra-tools/distinfo (nonexistent) +++ biology/sra-tools/distinfo (working copy) @@ -0,0 +1,5 @@ +TIMESTAMP = 1505268073 +SHA256 (ncbi-sra-tools-2.8.2-3_GH0.tar.gz) = d04e5fd735c3987c3497369844e20c1ae38a88867c36154798f072f19a8792fa +SIZE (ncbi-sra-tools-2.8.2-3_GH0.tar.gz) = 3992033 +SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2 +SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187 Property changes on: biology/sra-tools/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/Makefile.bsd =================================================================== --- biology/sra-tools/files/Makefile.bsd (nonexistent) +++ biology/sra-tools/files/Makefile.bsd (working copy) @@ -0,0 +1,75 @@ +# =========================================================================== +# +# 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 + +# copy without following symlinks +COPY = cp -P Property changes on: biology/sra-tools/files/Makefile.bsd ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_Makefile.clang =================================================================== --- biology/sra-tools/files/patch-build_Makefile.clang (nonexistent) +++ biology/sra-tools/files/patch-build_Makefile.clang (working copy) @@ -0,0 +1,35 @@ +--- build/Makefile.clang.orig 2017-08-03 16:17:04 UTC ++++ build/Makefile.clang +@@ -22,25 +22,27 @@ + # + # =========================================================================== + ++CCNAME ?= clang ++CXXNAME ?= clang++ + + # compilers +-CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \ ++CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \ + $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD +-CP = @ $(TOP)/build/cc.sh $(OS) 'clang++ -c' \ ++CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \ + $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD + + # C preprocessor +-PP = gcc -E $(CFLAGS) ++PP = $(CCNAME) -E $(CFLAGS) + + # linkers +-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \ ++LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \ + --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ + $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ + -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR) + + LPFLAGS = $(LDFLAGS) + +-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \ ++LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \ + --build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \ + $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ + -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR) Property changes on: biology/sra-tools/files/patch-build_Makefile.clang ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_Makefile.env =================================================================== --- biology/sra-tools/files/patch-build_Makefile.env (nonexistent) +++ biology/sra-tools/files/patch-build_Makefile.env (working copy) @@ -0,0 +1,25 @@ +--- build/Makefile.env.orig 2017-08-03 16:17:04 UTC ++++ build/Makefile.env +@@ -346,6 +346,9 @@ endif + ifneq (,$(MAGIC_LIBDIR)) + LDPATHS += -L$(MAGIC_LIBDIR) + endif ++ifneq (,$(MBEDTLS_LIBDIR)) ++ LDPATHS += -L$(MBEDTLS_LIBDIR) ++endif + ifneq (,$(FUSE_LIBDIR)) + LDPATHS += -L$(FUSE_LIBDIR) + endif +@@ -356,9 +359,9 @@ DLLX ?= $(SHLX) + ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX) + + # default tool parameters +-CFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) +-CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) +-LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) ++CFLAGS = $(PKGCFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) ++CPFLAGS = $(CXXFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) ++LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) + + #------------------------------------------------------------------------------- + # runtests Property changes on: biology/sra-tools/files/patch-build_Makefile.env ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_Makefile.gcc =================================================================== --- biology/sra-tools/files/patch-build_Makefile.gcc (nonexistent) +++ biology/sra-tools/files/patch-build_Makefile.gcc (working copy) @@ -0,0 +1,35 @@ +--- build/Makefile.gcc.orig 2017-08-03 16:17:04 UTC ++++ build/Makefile.gcc +@@ -22,25 +22,27 @@ + # + # =========================================================================== + ++CCNAME ?= gcc ++CXXNAME ?= g++ + + # compilers +-CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \ ++CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \ + $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD +-CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \ ++CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \ + $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD + + # C preprocessor +-PP = gcc -E $(CFLAGS) ++PP = $(CCNAME) -E $(CFLAGS) + + # linkers +-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ ++LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \ + --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ + $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ + -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR) + + LPFLAGS = $(LDFLAGS) + +-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ ++LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \ + --build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \ + $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ + -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR) Property changes on: biology/sra-tools/files/patch-build_Makefile.gcc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_Makefile.install =================================================================== --- biology/sra-tools/files/patch-build_Makefile.install (nonexistent) +++ biology/sra-tools/files/patch-build_Makefile.install (working copy) @@ -0,0 +1,54 @@ +--- build/Makefile.install.orig 2017-08-03 16:17:04 UTC ++++ build/Makefile.install +@@ -52,14 +52,14 @@ installexes: + @ echo "Installing executables to $(INST_BINDIR)/..." + @ mkdir -p $(INST_BINDIR) + @ $(MAKE) -s --no-print-directory -f $(TOP)/build/Makefile.install $(TOOLS_TO_INSTALL) +- @ printf "Installing magic file..." +- @ $(COPY) $(TOP)/tools/copycat/magic $(INST_BINDIR) && echo "done" ++ @ echo "Renaming the executable kget to vdb-get to avoid possible conflict" ++ @ mv $(INST_BINDIR)/kget $(INST_BINDIR)/vdb-get + + $(TOOLS_TO_INSTALL): + @ printf "Installing $@..." + @ # ignore missing tools + @ - ( test -f $(BINDIR)/$@$(EXEX) || ( echo "not found" && false ) ) && \ +- $(COPY) $(BINDIR)/$@$(EXEX) $(BINDIR)/$@$(VERSION_EXEX) $(BINDIR)/$@$(MAJVERS_EXEX) $(INST_BINDIR) && \ ++ $(BSD_INSTALL_PROGRAM) $(BINDIR)/$@$(EXEX) $(INST_BINDIR) && \ + echo "done" + + ifeq (linux, $(OS)) +@@ -102,22 +102,22 @@ ifeq (true, $(LINUX_ROOT)) + @ #TODO: check version of the files above + else + @ # install configuration file(s) +- @ printf "Installing configuration files to $(INST_BINDIR)/ncbi/..." +- ( mkdir -p $(INST_BINDIR)/ncbi && \ +- cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(INST_BINDIR)/ncbi/ ; \ ++ @ printf "Installing configuration files to $(INST_ETCDIR)/ncbi/..." ++ ( mkdir -p $(INST_ETCDIR)/ncbi && \ ++ cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(INST_ETCDIR)/ncbi/ ; \ + if [ -f $(BINDIR)/ncbi/default.kfg ] ; then \ +- if [ -f $(INST_BINDIR)/ncbi/default.kfg ] ; then \ +- mv -v $(INST_BINDIR)/ncbi/default.kfg \ +- $(INST_BINDIR)/ncbi/default.kfg.orig; \ ++ if [ -f $(INST_ETCDIR)/ncbi/default.kfg ] ; then \ ++ mv -v $(INST_ETCDIR)/ncbi/default.kfg \ ++ $(INST_ETCDIR)/ncbi/default.kfg.orig; \ + fi; \ +- cp -p $(BINDIR)/ncbi/default.kfg $(INST_BINDIR)/ncbi ; \ ++ cp -p $(BINDIR)/ncbi/default.kfg $(INST_ETCDIR)/ncbi ; \ + fi; \ + if [ -f $(BINDIR)/ncbi/certs.kfg ] ; then \ +- if [ -f $(INST_BINDIR)/ncbi/certs.kfg ] ; then \ +- mv -v $(INST_BINDIR)/ncbi/certs.kfg \ +- $(INST_BINDIR)/ncbi/certs.kfg.orig; \ ++ if [ -f $(INST_ETCDIR)/ncbi/certs.kfg ] ; then \ ++ mv -v $(INST_ETCDIR)/ncbi/certs.kfg \ ++ $(INST_ETCDIR)/ncbi/certs.kfg.orig; \ + fi; \ +- cp -p $(BINDIR)/ncbi/certs.kfg $(INST_BINDIR)/ncbi ; \ ++ cp -p $(BINDIR)/ncbi/certs.kfg $(INST_ETCDIR)/ncbi ; \ + fi ) && echo done + endif + Property changes on: biology/sra-tools/files/patch-build_Makefile.install ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_Makefile.shell =================================================================== --- biology/sra-tools/files/patch-build_Makefile.shell (nonexistent) +++ biology/sra-tools/files/patch-build_Makefile.shell (working copy) @@ -0,0 +1,31 @@ +--- build/Makefile.shell.orig 2017-08-03 16:17:04 UTC ++++ build/Makefile.shell +@@ -41,6 +41,9 @@ ifeq (Linux, $(UNAME)) + $(error "*** File '$(EXECMDF)' is missing. Please run $(TOP)/configure") + endif + endif ++ifeq (FreeBSD, $(UNAME)) ++ HOST_OS = bsd ++endif + ifeq (SunOS, $(UNAME)) + HOST_OS = sun + ARCHITECTURES = x86_64 i386 +@@ -96,6 +99,9 @@ else + ifeq (x86_64, $(MARCH)) + HOST_ARCH = x86_64 + endif ++ ifeq (amd64, $(MARCH)) ++ HOST_ARCH = x86_64 ++ endif + ifeq (i86pc, $(MARCH)) + HOST_ARCH = x86_64 + ARCHITECTURES = x86_64 i386 +@@ -106,7 +112,7 @@ else + endif + endif + +-ARCH = $(HOST_ARCH) ++override ARCH = $(HOST_ARCH) + REMOTE_ARCH = $(ARCH) + + # pick up dependencies from object directory Property changes on: biology/sra-tools/files/patch-build_Makefile.shell ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_ld.bsd.clang.sh =================================================================== --- biology/sra-tools/files/patch-build_ld.bsd.clang.sh (nonexistent) +++ biology/sra-tools/files/patch-build_ld.bsd.clang.sh (working copy) @@ -0,0 +1,18 @@ +--- build/ld.bsd.clang.sh.orig 2017-10-27 02:08:53 UTC ++++ build/ld.bsd.clang.sh +@@ -33,13 +33,8 @@ LD_REF_SYMBOLS="-Wl,-no-whole-archive" + + # build command + DLIB_CMD="$LD -shared" +- +-#EXE_CMD="$LD -static-libstdc++ -static-libgcc" +-source "${0%exe.sh}exe_cmd.sh" # EXE_CMD is defined in build/ld.linux.exe_cmd.sh +- +-EXE_STATIC_CMD="$EXE_CMD" +-#EXE_CMD="$LD" +-#EXE_STATIC_CMD="$LD -static" ++EXE_CMD="$LD" ++EXE_STATIC_CMD="$LD -static" + + # versioned output + if [ "$VERS" = "" ] Property changes on: biology/sra-tools/files/patch-build_ld.bsd.clang.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_ld.bsd.dlib.sh =================================================================== --- biology/sra-tools/files/patch-build_ld.bsd.dlib.sh (nonexistent) +++ biology/sra-tools/files/patch-build_ld.bsd.dlib.sh (working copy) @@ -0,0 +1,31 @@ +--- build/ld.bsd.dlib.sh.orig 2017-10-27 02:08:53 UTC ++++ build/ld.bsd.dlib.sh +@@ -51,8 +51,8 @@ case "$LD" in + g*) + source "${0%dlib.sh}gcc.sh" + ;; +-i*) +- source "${0%dlib.sh}icc.sh" ++c*) ++ source "${0%dlib.sh}clang.sh" + ;; + *) + echo "$SELF_NAME: unrecognized ld tool - '$LD'" +@@ -100,7 +100,7 @@ then + # always load libdl as shared library + load-ref-symbols + load-dynamic +- CMD="$CMD -ldl" ++# CMD="$CMD -ldl" + ;; + + -l*) +@@ -275,7 +275,7 @@ then + fi + + # add in xml +-if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null ++if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.bsd.$ARCH > /dev/null + then + if [ $HAVE_XML -ne 0 ] + then Property changes on: biology/sra-tools/files/patch-build_ld.bsd.dlib.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_ld.bsd.exe.sh =================================================================== --- biology/sra-tools/files/patch-build_ld.bsd.exe.sh (nonexistent) +++ biology/sra-tools/files/patch-build_ld.bsd.exe.sh (working copy) @@ -0,0 +1,44 @@ +--- build/ld.bsd.exe.sh.orig 2017-10-27 02:08:53 UTC ++++ build/ld.bsd.exe.sh +@@ -51,8 +51,8 @@ case "$LD" in + g*) + source "${0%exe.sh}gcc.sh" + ;; +-i*) +- source "${0%exe.sh}icc.sh" ++c*) ++ source "${0%exe.sh}clang.sh" + ;; + *) + echo "$SELF_NAME: unrecognized ld tool - '$LD'" +@@ -113,7 +113,7 @@ then + # always load libdl as shared library + load-ref-symbols + load-dynamic +- CMD="$CMD -ldl" ++# CMD="$CMD -ldl" + ;; + + -l*) +@@ -294,18 +294,11 @@ then + fi + + # add in xml +-if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null ++if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.bsd.$ARCH > /dev/null + then +- if grep -q XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null ++ if grep -q XML2_LIBDIR ${BUILD_DIR}/Makefile.config.bsd.$ARCH > /dev/null + then +- if grep -q 'OS_DISTRIBUTOR = Ubuntu' ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null +- then +- ##### Do not link libxml2 statically on Ubuntu: it does not compile +- XMLLIBDIR="-L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')" +- else +- ##### Link libxml2 statically on all linux-es except Ubuntu +- XMLLIBDIR="-Wl,-Bstatic -L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')" +- fi ++ XMLLIBDIR="-L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.bsd.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')" + fi + if [ $HAVE_XML -ne 0 ] + then Property changes on: biology/sra-tools/files/patch-build_ld.bsd.exe.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_ld.bsd.gcc.sh =================================================================== --- biology/sra-tools/files/patch-build_ld.bsd.gcc.sh (nonexistent) +++ biology/sra-tools/files/patch-build_ld.bsd.gcc.sh (working copy) @@ -0,0 +1,18 @@ +--- build/ld.bsd.gcc.sh.orig 2017-10-27 02:08:53 UTC ++++ build/ld.bsd.gcc.sh +@@ -33,13 +33,8 @@ LD_REF_SYMBOLS="-Wl,-no-whole-archive" + + # build command + DLIB_CMD="$LD -shared" +- +-#EXE_CMD="$LD -static-libstdc++ -static-libgcc" +-source "${0%exe.sh}exe_cmd.sh" # EXE_CMD is defined in build/ld.linux.exe_cmd.sh +- +-EXE_STATIC_CMD="$EXE_CMD" +-#EXE_CMD="$LD" +-#EXE_STATIC_CMD="$LD -static" ++EXE_CMD="$LD" ++EXE_STATIC_CMD="$LD -static" + + # versioned output + if [ "$VERS" = "" ] Property changes on: biology/sra-tools/files/patch-build_ld.bsd.gcc.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-build_ld.sh =================================================================== --- biology/sra-tools/files/patch-build_ld.sh (nonexistent) +++ biology/sra-tools/files/patch-build_ld.sh (working copy) @@ -0,0 +1,60 @@ +--- build/ld.sh.orig 2017-10-27 02:08:53 UTC ++++ build/ld.sh +@@ -68,6 +68,8 @@ HAVE_M=0 + NEED_M=1 + HAVE_XML=0 + NEED_XML=0 ++HAVE_MBEDTLS=0 ++NEED_MBEDTLS=0 + HAVE_KFC=0 + HAVE_KAPP=0 + HAVE_NCBI_VDB=0 +@@ -294,11 +296,12 @@ do + LIBS="$LIBS $1" + ;; + +- -[lds]ncbi-vdb) ++ -[lds]ncbi-vdb*) + HAVE_NCBI_VDB=1 + KPROC=4 +- HAVE_GZIP=1 +- HAVE_BZIP=1 ++ NEED_GZIP=1 ++ NEED_BZIP=1 ++ NEED_MBEDTLS=1 + HAVE_KFC=1 + NEED_M=1 + +@@ -310,18 +313,19 @@ do + -[lds]ncbi-ngs-c++) + HAVE_NCBI_VDB=1 + KPROC=4 +- HAVE_GZIP=1 +- HAVE_BZIP=1 ++ NEED_GZIP=1 ++ NEED_BZIP=1 + HAVE_KFC=1 + NEED_M=1 + NEED_XML=$CONFIGURE_FOUND_XML2 + LIBS="$LIBS $1" + ;; +- -[lds]ncbi-wvdb) ++ -[lds]ncbi-wvdb*) + HAVE_NCBI_WVDB=1 + KPROC=4 +- HAVE_GZIP=1 +- HAVE_BZIP=1 ++ NEED_GZIP=1 ++ NEED_BZIP=1 ++ NEED_MBEDTLS=1 + HAVE_KFC=1 + NEED_M=16 + NEED_XML=$CONFIGURE_FOUND_XML2 +@@ -515,6 +519,7 @@ fi + # supply missing libraries + [ $HAVE_GZIP -eq 0 ] && [ $NEED_GZIP -ne 0 ] && LIBS="$LIBS -lz" + [ $HAVE_BZIP -eq 0 ] && [ $NEED_BZIP -ne 0 ] && LIBS="$LIBS -lbz2" ++[ $HAVE_MBEDTLS -eq 0 ] && [ $NEED_MBEDTLS -ne 0 ] && LIBS="$LIBS -lmbedtls -lmbedcrypto -lmbedx509" + [ $HAVE_DL -eq 0 ] && [ $NEED_DL -ne 0 ] && LIBS="$LIBS -ldl" + [ $HAVE_M -eq 0 ] && [ $NEED_M -ne 0 ] && HAVE_M=16 + [ $HAVE_XML -eq 0 ] && [ $NEED_XML -ne 0 ] && HAVE_XML=32 Property changes on: biology/sra-tools/files/patch-build_ld.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-setup_konfigure.perl =================================================================== --- biology/sra-tools/files/patch-setup_konfigure.perl (nonexistent) +++ biology/sra-tools/files/patch-setup_konfigure.perl (working copy) @@ -0,0 +1,252 @@ +--- setup/konfigure.perl.orig 2017-08-03 16:17:04 UTC ++++ setup/konfigure.perl +@@ -186,7 +186,7 @@ if ($OPT{'help'}) { + foreach (@ARGV) { + @_ = split('='); + next if ($#_ != 1); +- $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS'); ++ $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS'); + } + + println "Configuring $PACKAGE_NAME package"; +@@ -198,7 +198,7 @@ print "checking system type... " unless + my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch(); + println $OSTYPE unless ($AUTORUN); + +-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { ++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { + println "configure: error: unsupported system '$OSTYPE'"; + exit 1; + } +@@ -213,7 +213,7 @@ if ($OS eq 'linux') { + + print "checking machine architecture... " unless ($AUTORUN); + println $MARCH unless ($AUTORUN); +-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) { ++unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i) { + println "configure: error: unsupported architecture '$OSTYPE'"; + exit 1; + } +@@ -298,7 +298,7 @@ print "checking for supported architectu + + my $BITS; + +-if ($MARCH =~ /x86_64/i) { ++if ($MARCH =~ /(x86_|amd)64/i) { + $BITS = 64; + } elsif ($MARCH eq 'fat86') { + $BITS = '32_64'; +@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) { + $EXEX = ''; + $OSINC = 'unix'; + $TOOLS = 'clang' unless ($TOOLS); ++} elsif ($OSTYPE =~ /freebsd/i) { ++ $LPFX = 'lib'; ++ $OBJX = 'o'; ++ $LOBX = 'pic.o'; ++ $LIBX = 'a'; ++ $SHLX = 'so'; ++ $EXEX = ''; ++ $OSINC = 'unix'; ++ unless ($TOOLS) { ++ $TOOLS = 'clang'; ++ $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS}); ++ } + } elsif ($OSTYPE eq 'win') { + $TOOLS = 'vc++'; + } else { +@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M + + print "checking for supported tool chain... " unless ($AUTORUN); + ++$CC = $OPT{CC } if ($OPT{CC }); + $CPP = $OPT{CXX } if ($OPT{CXX }); + $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS}); + + if ($TOOLS =~ /gcc$/) { + $CPP = 'g++' unless ($CPP); +- $CC = "$TOOLS -c"; ++ $CC = 'gcc' unless ($CC); ++ $LD = $CC; ++ $CC = "$CC -c"; + $CP = "$CPP -c"; + $AR = 'ar rc'; + $ARX = 'ar x'; + $ARLS = 'ar t'; +- $LD = $TOOLS; + $LP = $CPP; + + $DBG = '-g -DDEBUG'; +@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) { + $MD = '-MD'; + } elsif ($TOOLS eq 'clang') { + $CPP = 'clang++' unless ($CPP); +- $CC = 'clang -c'; +- my $versionMin = '-mmacosx-version-min=10.6'; ++ $CC = 'clang' unless ($CC); ++ $LD = $CC; ++ $CC = "$CC -c"; ++ my $versionMin = ''; ++ $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i); + $CP = "$CPP -c $versionMin"; + if ($BITS ne '32_64') { + $ARCH_FL = '-arch i386' if ($BITS == 32); + $OPT = '-O3'; + $AR = 'ar rc'; +- $LD = "clang $ARCH_FL"; ++ $LD = "$LD $ARCH_FL"; + $LP = "$CPP $versionMin $ARCH_FL"; + } else { + $MAKE_MANIFEST = '( echo "$^" > $@/manifest )'; + $ARCH_FL = '-arch i386 -arch x86_64'; + $OPT = '-O3'; + $AR = 'libtool -static -o'; +- $LD = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; ++ $LD = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; + $LP = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; + } + $ARX = 'ar x'; +@@ -759,13 +776,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os + # install paths + EndText + +- L($F, "INST_BINDIR = $OPT{'bindir'}" ) if ($OPT{'bindir'}); +- L($F, "INST_LIBDIR = $OPT{'libdir'}" ) if ($OPT{'libdir'}); +- L($F, "INST_INCDIR = $OPT{'includedir'}" ) if ($OPT{'includedir'}); +- L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'}); +- L($F, "INST_SHAREDIR = $OPT{'sharedir'}" ) if ($OPT{'sharedir'}); +- L($F, "INST_JARDIR = $OPT{'javadir'}" ) if ($OPT{'javadir'}); +- L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'}); ++ L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}" ) if ($OPT{'bindir'}); ++ L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}" ) if ($OPT{'libdir'}); ++ L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}" ) if ($OPT{'includedir'}); ++ L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'}); ++ L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}" ) if ($OPT{'sharedir'}); ++ L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}" ) if ($OPT{'javadir'}); ++ L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'}); + + my ($E_VERSION_SHLX, $VERSION_SHLX, + $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX); +@@ -829,7 +846,7 @@ MAJMIN_EXEX = \$(EXEX).\$(MAJMIN) + MAJVERS_EXEX = \$(EXEX).\$(MAJVERS) + + # system architecture and wordsize +-ARCH = $ARCH ++override ARCH = $ARCH + EndText + + L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH); +@@ -864,7 +881,7 @@ EndText + } + L($F, "PIC = $PIC") if ($PIC); + if ($PKG{LNG} eq 'C') { +- if ($TOOLS =~ /clang/i) { ++ if ($OSTYPE =~ /darwin/i) { + L($F, 'SONAME = -install_name ' . + '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); + L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\'); +@@ -975,7 +992,7 @@ EndText + L($F, '# directory rules'); + if ($PKG{LNG} eq 'C') { + L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) ' +- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):'); ++ . '$(OBJDIR) $(INST_LIBDIR):'); + T($F, 'mkdir -p $@'); + } elsif ($PKG{LNG} eq 'JAVA') { + # test if we have jni header path +@@ -1005,12 +1022,12 @@ EndText + L($F, 'export CONFIGURE_FOUND_XML2'); + L($F); + +- if ($OS eq 'linux' || $OS eq 'mac') { ++ if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') { + L($F, '# installation rules'); + L($F, +- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)'); ++ '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)'); + T($F, '@ echo -n "installing \'$(@F)\'... "'); +- T($F, '@ if cp $^ $@ && chmod 644 $@; \\'); ++ T($F, '@ if $(BSD_INSTALL_DATA) $^ $@; \\'); + T($F, ' then \\'); + T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' + . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) ' +@@ -1019,7 +1036,7 @@ EndText + T($F, ' ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) ' + . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\'); + T($F, ' ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' . +- '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));' ++ '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));' + . ' \\'); + T($F, ' echo success; \\'); + T($F, ' else \\'); +@@ -1029,15 +1046,15 @@ EndText + L($F); + + L($F, +- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)'); ++ '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)'); + T($F, '@ echo -n "installing \'$(@F)\'... "'); +- T($F, '@ if cp $^ $@ && chmod 755 $@; \\'); ++ T($F, '@ if $(BSD_INSTALL_LIB) $^ $@; \\'); + T($F, ' then \\'); + if ($OS ne 'mac') { + T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' + . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@); \\'); + } +- if ($OS eq 'linux') { ++ if ($OS eq 'linux' || $OS eq 'bsd') { + T($F, ' ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\'); + } elsif ($OS eq 'mac') { + T($F, ' ln -sf $(@F) ' +@@ -1056,7 +1073,7 @@ EndText + + L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)'); + T($F, '@ echo -n "installing \'$(@F)\'... "'); +- T($F, '@ if cp $^ $@ && chmod 755 $@; \\'); ++ T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@; \\'); + T($F, ' then \\'); + T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' + . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@); \\'); +@@ -1338,7 +1355,7 @@ sub find_in_dir { + ++$found; + } + if (! $found) { +- my $libdir = File::Spec->catdir($dir, 'lib' . $BITS); ++ my $libdir = File::Spec->catdir($dir, 'lib'); + my $f = File::Spec->catdir($libdir, $lib); + print "\tchecking $f\n\t" if ($OPT{'debug'}); + if (-e $f) { +@@ -1480,12 +1497,12 @@ sub find_lib { + + sub check_compiler { + my ($t, $n, $I, @l) = @_; +- my $tool = $TOOLS; ++ my $tool = $CC; + + if ($t eq 'L') { + print "checking for $n library... "; + } elsif ($t eq 'O') { +- if ($tool && ($tool =~ /gcc$/ || $tool =~ /g\+\+$/)) { ++ if ($tool && ($tool =~ /gcc/ || $tool =~ /g\+\+/)) { + print "checking whether $tool accepts $n... "; + } else { + return; +@@ -1515,6 +1532,9 @@ sub check_compiler { + } elsif ($n eq 'magic') { + $library = '-lmagic'; + $log = '#include \n int main() { magic_open (0); }\n' ++ } elsif ($n eq 'mbedtls') { ++ $library = '-lmbedtls'; ++ $log = '#include \n int main() { mbedtls_version_get_string(0); }\n' + } elsif ($n eq 'xml2') { + $library = '-lxml2'; + $library .= ' -liconv' if ($OS eq 'mac'); +@@ -1551,7 +1571,7 @@ sub check_compiler { + my $l = $l [ $i ]; + next if ( $l && ! -d $l ); + my $gcc = "| $tool -xc $flags " . ($I ? "-I$I " : ' ') +- . ($l ? "-L$l " : ' ') . "- $library"; ++ . ($l ? "-L$l " : ' ') . "-o a.out - $library"; + $gcc .= ' 2> /dev/null' unless ($OPT{'debug'}); + + open GCC, $gcc or last; Property changes on: biology/sra-tools/files/patch-setup_konfigure.perl ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-setup_os-arch.prl =================================================================== --- biology/sra-tools/files/patch-setup_os-arch.prl (nonexistent) +++ biology/sra-tools/files/patch-setup_os-arch.prl (working copy) @@ -0,0 +1,20 @@ +--- setup/os-arch.prl.orig 2017-08-03 16:17:04 UTC ++++ setup/os-arch.prl +@@ -11,6 +11,8 @@ sub OsArch { + chomp $UNAME; + if ($UNAME =~ /Darwin/) { + $HOST_OS = 'mac'; ++ } elsif ($UNAME =~ /.*BSD/) { ++ $HOST_OS = 'bsd'; + } elsif ($UNAME =~ /Linux/) { + $HOST_OS = 'linux'; + } elsif ($UNAME =~ /SunOS/) { +@@ -49,6 +51,8 @@ sub OsArch { + } + } elsif ($MARCH =~ /x86_64/) { + $HOST_ARCH = 'x86_64'; ++ } elsif ($MARCH =~ /amd64/) { ++ $HOST_ARCH = 'x86_64'; + } elsif ($MARCH =~ /i86pc/) { + $HOST_ARCH = 'x86_64'; + @ARCHITECTURES = qw(x86_64 i386); Property changes on: biology/sra-tools/files/patch-setup_os-arch.prl ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-setup_package.prl =================================================================== --- biology/sra-tools/files/patch-setup_package.prl (nonexistent) +++ biology/sra-tools/files/patch-setup_package.prl (working copy) @@ -0,0 +1,26 @@ +--- setup/package.prl.orig 2017-08-03 16:17:04 UTC ++++ setup/package.prl +@@ -12,6 +12,7 @@ sub PKG { ( LNG => 'C', + sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include' , }, + { name => 'hdf5' , Include => '/usr/include' , }, + { name => 'magic', Include => '/usr/include' , }, ++ { name => 'mbedtls', Include => '/usr/include' , }, + { name => 'xml2' , Include => '/usr/include/libxml2', } ) } + sub REQ { ( + { name => 'ngs-sdk', +@@ -58,6 +59,15 @@ sub REQ { ( + origin => 'E', + type => 'LIO', + }, ++ { name => 'mbedtls', ++ option => 'with-mbedtls-prefix', ++ origin => 'E', ++ type => 'LIO', ++ pkgpath => '/usr', ++ usrpath => '$HOME', ++ include => 'mbedtls/config.h', ++ lib => 'libmbedtls.so', ++ }, + { name => 'xml2', + option => 'with-xml2-prefix', + origin => 'E', Property changes on: biology/sra-tools/files/patch-setup_package.prl ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-test_general-loader_VDB-3250_prepare__test__data.sh =================================================================== --- biology/sra-tools/files/patch-test_general-loader_VDB-3250_prepare__test__data.sh (nonexistent) +++ biology/sra-tools/files/patch-test_general-loader_VDB-3250_prepare__test__data.sh (working copy) @@ -0,0 +1,11 @@ +--- test/general-loader/VDB-3250/prepare_test_data.sh.orig 2017-10-27 02:08:53 UTC ++++ test/general-loader/VDB-3250/prepare_test_data.sh +@@ -160,7 +160,7 @@ test_check_exe LOADER_EXE $BIN_DIR/gener + # + cd $TEST_DATA_DIR + +-_exec make ++_exec gmake + + test_check_exe PREPARER_EXE $TEST_BIN_DIR/prepare_test_data + test_check_exe CHECKER_EXE $TEST_BIN_DIR/check_test_result Property changes on: biology/sra-tools/files/patch-test_general-loader_VDB-3250_prepare__test__data.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-test_kar_kar-test.sh =================================================================== --- biology/sra-tools/files/patch-test_kar_kar-test.sh (nonexistent) +++ biology/sra-tools/files/patch-test_kar_kar-test.sh (working copy) @@ -0,0 +1,22 @@ +--- test/kar/kar-test.sh.orig 2017-10-27 02:08:53 UTC ++++ test/kar/kar-test.sh +@@ -38,6 +38,10 @@ case $UNAME in + (Linux) + OS=linux + ;; ++ (FreeBSD) ++ OS=bsd ++ MD5TOOL=/sbin/md5 ++ ;; + (Darwin) + OS=mac + MD5TOOL=/sbin/md5 +@@ -129,7 +133,7 @@ test_create_options () + exit 1 + fi + ;; +- (Darwin) ++ (Darwin|FreeBSD) + if [ ! -x $MD5TOOL ] + then + echo "could not locate executable md5 tool" Property changes on: biology/sra-tools/files/patch-test_kar_kar-test.sh ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c =================================================================== --- biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c (nonexistent) +++ biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c (working copy) @@ -0,0 +1,10 @@ +--- tools/bam-loader/loader-imp.c.orig 2017-08-03 16:17:04 UTC ++++ tools/bam-loader/loader-imp.c +@@ -73,6 +73,7 @@ + + #include + #include ++#include + #include + #include + #include Property changes on: biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_copycat_Makefile =================================================================== --- biology/sra-tools/files/patch-tools_copycat_Makefile (nonexistent) +++ biology/sra-tools/files/patch-tools_copycat_Makefile (working copy) @@ -0,0 +1,11 @@ +--- tools/copycat/Makefile.orig 2017-08-03 16:17:04 UTC ++++ tools/copycat/Makefile +@@ -92,7 +92,7 @@ COPYCAT_LIB = \ + -stk-version \ + -sncbi-vdb \ + -skff \ +- -smagic-static ++ -smagic + + + $(BINDIR)/copycat: $(COPYCAT_OBJ) Property changes on: biology/sra-tools/files/patch-tools_copycat_Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_copycat_ccfileformat.c =================================================================== --- biology/sra-tools/files/patch-tools_copycat_ccfileformat.c (nonexistent) +++ biology/sra-tools/files/patch-tools_copycat_ccfileformat.c (working copy) @@ -0,0 +1,19 @@ +--- tools/copycat/ccfileformat.c.orig 2017-08-03 16:17:04 UTC ++++ tools/copycat/ccfileformat.c +@@ -184,11 +184,11 @@ rc_t CCFileFormatMake (CCFileFormat ** p + KConfigRelease ( kfg ); + if ( rc == 0 ) + { +- char magicpath[1024]; +- size_t num_writ; +- rc = string_printf ( magicpath, sizeof ( magicpath ), &num_writ, "%S/magic", bindir ); +- StringWhack ( bindir ); +- if ( rc == 0 ) ++// char magicpath[1024]; ++// size_t num_writ; ++// rc = string_printf ( magicpath, sizeof ( magicpath ), &num_writ, "%S/magic", bindir ); ++// StringWhack ( bindir ); ++// if ( rc == 0 ) + { + rc = KExtFileFormatMake (&self->ext, exttable, sizeof (exttable) - 1, + formattable, sizeof (formattable) - 1); Property changes on: biology/sra-tools/files/patch-tools_copycat_ccfileformat.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_fastq-loader_common-writer.c =================================================================== --- biology/sra-tools/files/patch-tools_fastq-loader_common-writer.c (nonexistent) +++ biology/sra-tools/files/patch-tools_fastq-loader_common-writer.c (working copy) @@ -0,0 +1,10 @@ +--- tools/fastq-loader/common-writer.c.orig 2017-08-03 16:17:04 UTC ++++ tools/fastq-loader/common-writer.c +@@ -58,6 +58,7 @@ + + #include + #include ++#include + #include + + #define USE_READER_THREAD (1) Property changes on: biology/sra-tools/files/patch-tools_fastq-loader_common-writer.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_general-loader_gw-dumper.cpp =================================================================== --- biology/sra-tools/files/patch-tools_general-loader_gw-dumper.cpp (nonexistent) +++ biology/sra-tools/files/patch-tools_general-loader_gw-dumper.cpp (working copy) @@ -0,0 +1,10 @@ +--- tools/general-loader/gw-dumper.cpp.orig 2017-08-03 16:17:04 UTC ++++ tools/general-loader/gw-dumper.cpp +@@ -34,7 +34,6 @@ + + #include + #include +-#include + #include + #include + Property changes on: biology/sra-tools/files/patch-tools_general-loader_gw-dumper.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_pacbio-load_Makefile =================================================================== --- biology/sra-tools/files/patch-tools_pacbio-load_Makefile (nonexistent) +++ biology/sra-tools/files/patch-tools_pacbio-load_Makefile (working copy) @@ -0,0 +1,11 @@ +--- tools/pacbio-load/Makefile.orig 2017-08-03 16:17:04 UTC ++++ tools/pacbio-load/Makefile +@@ -105,7 +105,7 @@ PACBIO_LOAD_LIB = \ + -stk-version \ + -skdf5 \ + -sload \ +- -shdf5 \ ++ -lhdf5 \ + -sncbi-wvdb \ + -sm \ + Property changes on: biology/sra-tools/files/patch-tools_pacbio-load_Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/files/patch-tools_vdb-decrypt_Makefile =================================================================== --- biology/sra-tools/files/patch-tools_vdb-decrypt_Makefile (nonexistent) +++ biology/sra-tools/files/patch-tools_vdb-decrypt_Makefile (working copy) @@ -0,0 +1,11 @@ +--- tools/vdb-decrypt/Makefile.orig 2017-08-03 16:17:04 UTC ++++ tools/vdb-decrypt/Makefile +@@ -25,7 +25,7 @@ + + default: std + +-USE_GCC_IF_ICC = 1 ++#USE_GCC_IF_ICC = 1 + + TOP ?= $(abspath ../..) + MODULE = tools/vdb-decrypt Property changes on: biology/sra-tools/files/patch-tools_vdb-decrypt_Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/pkg-descr =================================================================== --- biology/sra-tools/pkg-descr (nonexistent) +++ biology/sra-tools/pkg-descr (working copy) @@ -0,0 +1,18 @@ +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. + +WWW: https://github.com/ncbi/sra-tools/wiki Property changes on: biology/sra-tools/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: biology/sra-tools/pkg-plist =================================================================== --- biology/sra-tools/pkg-plist (nonexistent) +++ biology/sra-tools/pkg-plist (working copy) @@ -0,0 +1,41 @@ +bin/abi-dump +bin/abi-load +bin/align-info +bin/bam-load +bin/cache-mgr +bin/cg-load +bin/copycat +bin/fastdump +bin/fastq-dump +bin/fastq-load +bin/helicos-load +bin/illumina-dump +bin/illumina-load +bin/kar +bin/kdbmeta +bin/latf-load +bin/pacbio-load +bin/prefetch +bin/rcexplain +bin/sam-dump +bin/sff-dump +bin/sff-load +bin/sra-pileup +bin/sra-sort +bin/sra-stat +bin/srapath +bin/srf-load +bin/test-sra +bin/vdb-config +bin/vdb-copy +bin/vdb-decrypt +bin/vdb-dump +bin/vdb-encrypt +bin/vdb-get +bin/vdb-lock +bin/vdb-passwd +bin/vdb-unlock +bin/vdb-validate +etc/ncbi/certs.kfg +etc/ncbi/default.kfg +etc/ncbi/vdb-copy.kfg Property changes on: biology/sra-tools/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property