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(-)biology/sra-tools/Makefile (+69 lines)
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# $FreeBSD$
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3
PORTNAME=	sra-tools
4
DISTVERSION=	2.8.2-3
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CATEGORIES=	biology
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7
MAINTAINER=	mzaki@niid.go.jp
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COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
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LICENSE=	PD LGPL21+
11
LICENSE_COMB=	multi
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LICENSE_FILE_PD=	${WRKSRC}/LICENSE
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LICENSE_DISTFILES_LGPL21+ =
14
# The executables contain functions from biology/ncbi-vdb port,
15
# which is derived from a part of LGPL-licensed GNU C Library or Judy library.
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BUILD_DEPENDS=	bash:shells/bash \
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		${NONEXISTENT}:biology/ncbi-vdb:build \
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		${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
20
LIB_DEPENDS=	libxml2.so:textproc/libxml2 \
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		libhdf5.so:science/hdf5 \
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		libmbedtls.so:security/mbedtls
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USE_GITHUB=	yes
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GH_ACCOUNT=	ncbi
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USES=		compiler gmake perl5 shebangfix
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USE_PERL5=	build
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SHEBANG_GLOB=	*.sh *.pl
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GNU_CONFIGURE=	yes
32
VDBSRC_CMD=	${MAKE} -C ${.CURDIR}/../ncbi-vdb -V WRKSRC
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CONFIGURE_ARGS=	--with-ngs-sdk-prefix=${LOCALBASE} \
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		--with-ncbi-vdb-sources=$$(${VDBSRC_CMD}) \
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		--with-ncbi-vdb-build=$$(${VDBSRC_CMD})/${CONFIGURE_TARGET}/ncbi-vdb/ \
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		--with-xml2-prefix=${LOCALBASE} \
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		--with-hdf5-prefix=${LOCALBASE} \
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		--with-mbedtls-prefix=${LOCALBASE} \
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		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
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MAKE_ARGS=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
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		INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
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ONLY_FOR_ARCHS=	amd64 i386
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ONLY_FOR_ARCHS_REASON=	NCBI-VDB requires SSE2 instructions
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BROKEN_i386=	buggy output
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47
# for port developpers, building with these options may fail
48
OPTIONS_DEFINE=	DEBUG GCC OPTIMIZED_CFLAGS TEST
49
DEBUG_PREVENTS=	OPTIMIZED_CFLAGS
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DEBUG_CONFIGURE_WITH=	debug
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GCC_USE=	gcc=yes
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OPTIMIZED_CFLAGS_MAKE_ARGS_OFF=	OPT=""
53
TEST_TEST_TARGET=	test
54
TEST_USES=	python
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pre-patch:
57
	@${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/
58
	@for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done
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	@${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh
60
61
post-patch-TEST-on:
62
	${REINPLACE_CMD} -e 's#python#${PYTHON_CMD}#' ${WRKSRC}/test/kget/Makefile
63
64
post-configure:
65
	@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP
66
67
post-build-TEST-on:	do-test
68
69
.include <bsd.port.mk>
(-)biology/sra-tools/distinfo (+5 lines)
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TIMESTAMP = 1505268073
2
SHA256 (ncbi-sra-tools-2.8.2-3_GH0.tar.gz) = d04e5fd735c3987c3497369844e20c1ae38a88867c36154798f072f19a8792fa
3
SIZE (ncbi-sra-tools-2.8.2-3_GH0.tar.gz) = 3992033
4
SHA256 (ncbi-ngs-1.3.0_GH0.tar.gz) = 803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2
5
SIZE (ncbi-ngs-1.3.0_GH0.tar.gz) = 1089187
(-)biology/sra-tools/files/Makefile.bsd (+75 lines)
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# ===========================================================================
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#
3
#                            PUBLIC DOMAIN NOTICE
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#               National Center for Biotechnology Information
5
#
6
#  This software/database is a "United States Government Work" under the
7
#  terms of the United States Copyright Act.  It was written as part of
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#  the author's official duties as a United States Government employee and
9
#  thus cannot be copyrighted.  This software/database is freely available
10
#  to the public for use. The National Library of Medicine and the U.S.
11
#  Government have not placed any restriction on its use or reproduction.
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#
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#  Although all reasonable efforts have been taken to ensure the accuracy
14
#  and reliability of the software and data, the NLM and the U.S.
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#  Government do not and cannot warrant the performance or results that
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#  may be obtained by using this software or data. The NLM and the U.S.
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#  Government disclaim all warranties, express or implied, including
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#  warranties of performance, merchantability or fitness for any particular
19
#  purpose.
20
#
21
#  Please cite the author in any work or product based on this material.
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#
23
# ===========================================================================
24
25
26
# default compiler
27
ifeq (,$(COMP))
28
	COMP = clang
29
endif
30
31
# handle attempts to set cross-compilation architecture
32
# note that if your installation is set up for cross compilation,
33
# you can try to enable it on your own.
34
ifeq (i386,$(ARCH))
35
i386:
36
	@ true
37
x86_64:
38
	@ echo "FreeBSD builds do not support cross-compilation to this architecture"
39
endif
40
41
ifeq (x86_64,$(ARCH))
42
i386:
43
	@ echo "FreeBSD builds do not support cross-compilation to this architecture"
44
x86_64:
45
	@ true
46
endif
47
48
.PHONY: i386 x86_64
49
50
51
# library prefix
52
LPFX = lib
53
54
# file extensions
55
OBJX = o
56
LOBX = pic.o
57
LIBX = a
58
SHLX = so
59
60
# compilation defines
61
DEFINES	:= -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS)
62
63
# FreeBSD is a Unix variant; for most cases, linux sources do well
64
OS_DAD = linux
65
OS_GDAD = unix
66
67
# flex+bison: on Mac, use source-controlled generated .c/.h files
68
YACC = @ true
69
LEX = @ true
70
71
# build matrix
72
COMPILERS = CLANG GCC
73
74
# copy without following symlinks
75
COPY = cp -P
(-)biology/sra-tools/files/patch-build_Makefile.clang (+35 lines)
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--- build/Makefile.clang.orig	2017-08-03 16:17:04 UTC
2
+++ build/Makefile.clang
3
@@ -22,25 +22,27 @@
4
 #
5
 # ===========================================================================
6
 
7
+CCNAME  ?= clang
8
+CXXNAME ?= clang++
9
 
10
 # compilers
11
-CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \
12
+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \
13
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
14
-CP = @ $(TOP)/build/cc.sh $(OS) 'clang++ -c' \
15
+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \
16
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD
17
 
18
 # C preprocessor
19
-PP = gcc -E $(CFLAGS)
20
+PP = $(CCNAME) -E $(CFLAGS)
21
 
22
 # linkers
23
-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \
24
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \
25
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
26
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
27
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
28
 
29
 LPFLAGS = $(LDFLAGS)
30
 
31
-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \
32
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \
33
 	--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \
34
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
35
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
(-)biology/sra-tools/files/patch-build_Makefile.env (+25 lines)
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--- build/Makefile.env.orig	2017-08-03 16:17:04 UTC
2
+++ build/Makefile.env
3
@@ -346,6 +346,9 @@ endif
4
 ifneq (,$(MAGIC_LIBDIR))
5
 	LDPATHS += -L$(MAGIC_LIBDIR)
6
 endif
7
+ifneq (,$(MBEDTLS_LIBDIR))
8
+	LDPATHS += -L$(MBEDTLS_LIBDIR)
9
+endif
10
 ifneq (,$(FUSE_LIBDIR))
11
 	LDPATHS += -L$(FUSE_LIBDIR)
12
 endif
13
@@ -356,9 +359,9 @@ DLLX ?= $(SHLX)
14
 ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
15
 
16
 # default tool parameters
17
-CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
18
-CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
19
-LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
20
+CFLAGS	= $(PKGCFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
21
+CPFLAGS = $(CXXFLAGS) $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
22
+LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
23
 
24
 #-------------------------------------------------------------------------------
25
 # runtests
(-)biology/sra-tools/files/patch-build_Makefile.gcc (+35 lines)
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--- build/Makefile.gcc.orig	2017-08-03 16:17:04 UTC
2
+++ build/Makefile.gcc
3
@@ -22,25 +22,27 @@
4
 #
5
 # ===========================================================================
6
 
7
+CCNAME  ?= gcc
8
+CXXNAME ?= g++
9
 
10
 # compilers
11
-CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \
12
+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \
13
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
14
-CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \
15
+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \
16
 	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD
17
 
18
 # C preprocessor
19
-PP = gcc -E $(CFLAGS)
20
+PP = $(CCNAME) -E $(CFLAGS)
21
 
22
 # linkers
23
-LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
24
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \
25
 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
26
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
27
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
28
 
29
 LPFLAGS = $(LDFLAGS)
30
 
31
-LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
32
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \
33
 	--build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \
34
 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
35
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR):$(NGS_LIBDIR):$(VDB_LIBDIR):$(VDB_ILIBDIR)
(-)biology/sra-tools/files/patch-build_Makefile.install (+54 lines)
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1
--- build/Makefile.install.orig	2017-08-03 16:17:04 UTC
2
+++ build/Makefile.install
3
@@ -52,14 +52,14 @@ installexes: 
4
 	@ echo "Installing executables to $(INST_BINDIR)/..."
5
 	@ mkdir -p $(INST_BINDIR) 
6
 	@ $(MAKE) -s --no-print-directory -f $(TOP)/build/Makefile.install $(TOOLS_TO_INSTALL)
7
-	@ printf "Installing magic file..."
8
-	@ $(COPY) $(TOP)/tools/copycat/magic $(INST_BINDIR) && echo "done"
9
+	@ echo "Renaming the executable kget to vdb-get to avoid possible conflict"
10
+	@ mv $(INST_BINDIR)/kget $(INST_BINDIR)/vdb-get
11
 
12
 $(TOOLS_TO_INSTALL):
13
 	@ printf "Installing $@..."
14
 	@ # ignore missing tools
15
 	@ - ( test -f $(BINDIR)/$@$(EXEX) || ( echo "not found" && false ) ) && \
16
-      $(COPY) $(BINDIR)/$@$(EXEX) $(BINDIR)/$@$(VERSION_EXEX) $(BINDIR)/$@$(MAJVERS_EXEX) $(INST_BINDIR) && \
17
+      $(BSD_INSTALL_PROGRAM) $(BINDIR)/$@$(EXEX) $(INST_BINDIR) && \
18
       echo "done"
19
     
20
 ifeq (linux, $(OS))
21
@@ -102,22 +102,22 @@ ifeq (true, $(LINUX_ROOT))
22
 	@ #TODO: check version of the files above
23
 else    
24
 	@ # install configuration file(s)
25
-	@ printf "Installing configuration files to $(INST_BINDIR)/ncbi/..."
26
-	( mkdir -p $(INST_BINDIR)/ncbi && \
27
-	  cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(INST_BINDIR)/ncbi/ ; \
28
+	@ printf "Installing configuration files to $(INST_ETCDIR)/ncbi/..."
29
+	( mkdir -p $(INST_ETCDIR)/ncbi && \
30
+	  cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(INST_ETCDIR)/ncbi/ ; \
31
 	  if [ -f $(BINDIR)/ncbi/default.kfg ] ; then \
32
-	    if [ -f $(INST_BINDIR)/ncbi/default.kfg ] ; then \
33
-          mv -v $(INST_BINDIR)/ncbi/default.kfg \
34
-                $(INST_BINDIR)/ncbi/default.kfg.orig; \
35
+	    if [ -f $(INST_ETCDIR)/ncbi/default.kfg ] ; then \
36
+          mv -v $(INST_ETCDIR)/ncbi/default.kfg \
37
+                $(INST_ETCDIR)/ncbi/default.kfg.orig; \
38
 	    fi; \
39
-	    cp -p $(BINDIR)/ncbi/default.kfg $(INST_BINDIR)/ncbi ; \
40
+	    cp -p $(BINDIR)/ncbi/default.kfg $(INST_ETCDIR)/ncbi ; \
41
 	  fi; \
42
 	  if [ -f $(BINDIR)/ncbi/certs.kfg ] ; then \
43
-	    if [ -f $(INST_BINDIR)/ncbi/certs.kfg ] ; then \
44
-          mv -v $(INST_BINDIR)/ncbi/certs.kfg \
45
-                $(INST_BINDIR)/ncbi/certs.kfg.orig; \
46
+	    if [ -f $(INST_ETCDIR)/ncbi/certs.kfg ] ; then \
47
+          mv -v $(INST_ETCDIR)/ncbi/certs.kfg \
48
+                $(INST_ETCDIR)/ncbi/certs.kfg.orig; \
49
 	    fi; \
50
-	    cp -p $(BINDIR)/ncbi/certs.kfg $(INST_BINDIR)/ncbi ; \
51
+	    cp -p $(BINDIR)/ncbi/certs.kfg $(INST_ETCDIR)/ncbi ; \
52
 	  fi ) && echo done
53
 endif
54
 
(-)biology/sra-tools/files/patch-build_Makefile.shell (+31 lines)
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1
--- build/Makefile.shell.orig	2017-08-03 16:17:04 UTC
2
+++ build/Makefile.shell
3
@@ -41,6 +41,9 @@ ifeq (Linux, $(UNAME))
4
         	$(error "*** File '$(EXECMDF)' is missing. Please run $(TOP)/configure")
5
 	endif
6
 endif
7
+ifeq (FreeBSD, $(UNAME))
8
+	HOST_OS = bsd
9
+endif
10
 ifeq (SunOS, $(UNAME))
11
 	HOST_OS = sun
12
 	ARCHITECTURES = x86_64 i386
13
@@ -96,6 +99,9 @@ else
14
 	ifeq (x86_64, $(MARCH))
15
 		HOST_ARCH = x86_64
16
 	endif
17
+	ifeq (amd64, $(MARCH))
18
+		HOST_ARCH = x86_64
19
+	endif
20
 	ifeq (i86pc, $(MARCH))
21
 		HOST_ARCH = x86_64
22
 		ARCHITECTURES = x86_64 i386
23
@@ -106,7 +112,7 @@ else
24
 	endif
25
 endif
26
 
27
-ARCH = $(HOST_ARCH)
28
+override ARCH = $(HOST_ARCH)
29
 REMOTE_ARCH = $(ARCH)
30
 
31
 # pick up dependencies from object directory
(-)biology/sra-tools/files/patch-build_ld.bsd.clang.sh (+18 lines)
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1
--- build/ld.bsd.clang.sh.orig	2017-10-27 02:08:53 UTC
2
+++ build/ld.bsd.clang.sh
3
@@ -33,13 +33,8 @@ LD_REF_SYMBOLS="-Wl,-no-whole-archive"
4
 
5
 # build command
6
 DLIB_CMD="$LD -shared"
7
-
8
-#EXE_CMD="$LD -static-libstdc++ -static-libgcc"
9
-source "${0%exe.sh}exe_cmd.sh" # EXE_CMD is defined in build/ld.linux.exe_cmd.sh
10
-
11
-EXE_STATIC_CMD="$EXE_CMD"
12
-#EXE_CMD="$LD"
13
-#EXE_STATIC_CMD="$LD -static"
14
+EXE_CMD="$LD"
15
+EXE_STATIC_CMD="$LD -static"
16
 
17
 # versioned output
18
 if [ "$VERS" = "" ]
(-)biology/sra-tools/files/patch-build_ld.bsd.dlib.sh (+31 lines)
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1
--- build/ld.bsd.dlib.sh.orig	2017-10-27 02:08:53 UTC
2
+++ build/ld.bsd.dlib.sh
3
@@ -51,8 +51,8 @@ case "$LD" in
4
 g*)
5
     source "${0%dlib.sh}gcc.sh"
6
     ;;
7
-i*)
8
-    source "${0%dlib.sh}icc.sh"
9
+c*)
10
+    source "${0%dlib.sh}clang.sh"
11
     ;;
12
  *)
13
     echo "$SELF_NAME: unrecognized ld tool - '$LD'"
14
@@ -100,7 +100,7 @@ then
15
             # always load libdl as shared library
16
             load-ref-symbols
17
             load-dynamic
18
-            CMD="$CMD -ldl"
19
+#            CMD="$CMD -ldl"
20
             ;;
21
 
22
         -l*)
23
@@ -275,7 +275,7 @@ then
24
 fi
25
 
26
 # add in xml
27
-if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null
28
+if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.bsd.$ARCH > /dev/null
29
 then
30
     if [ $HAVE_XML -ne 0 ]
31
     then
(-)biology/sra-tools/files/patch-build_ld.bsd.exe.sh (+44 lines)
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1
--- build/ld.bsd.exe.sh.orig	2017-10-27 02:08:53 UTC
2
+++ build/ld.bsd.exe.sh
3
@@ -51,8 +51,8 @@ case "$LD" in
4
 g*)
5
     source "${0%exe.sh}gcc.sh"
6
     ;;
7
-i*)
8
-    source "${0%exe.sh}icc.sh"
9
+c*)
10
+    source "${0%exe.sh}clang.sh"
11
     ;;
12
 *)
13
     echo "$SELF_NAME: unrecognized ld tool - '$LD'"
14
@@ -113,7 +113,7 @@ then
15
             # always load libdl as shared library
16
             load-ref-symbols
17
             load-dynamic
18
-            CMD="$CMD -ldl"
19
+#            CMD="$CMD -ldl"
20
             ;;
21
 
22
         -l*)
23
@@ -294,18 +294,11 @@ then
24
 fi
25
 
26
 # add in xml
27
-if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null
28
+if grep -q HAVE_XML2 ${BUILD_DIR}/Makefile.config.bsd.$ARCH > /dev/null
29
 then
30
-    if grep -q XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null
31
+    if grep -q XML2_LIBDIR ${BUILD_DIR}/Makefile.config.bsd.$ARCH > /dev/null
32
     then
33
-        if grep -q 'OS_DISTRIBUTOR = Ubuntu' ${BUILD_DIR}/Makefile.config.linux.$ARCH > /dev/null
34
-        then
35
-            ##### Do not link libxml2 statically on Ubuntu: it does not compile
36
-            XMLLIBDIR="-L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')"
37
-        else
38
-            ##### Link libxml2 statically on all linux-es except Ubuntu
39
-            XMLLIBDIR="-Wl,-Bstatic -L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')"
40
-        fi
41
+        XMLLIBDIR="-L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.bsd.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')"
42
     fi
43
     if [ $HAVE_XML -ne 0 ]
44
     then
(-)biology/sra-tools/files/patch-build_ld.bsd.gcc.sh (+18 lines)
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1
--- build/ld.bsd.gcc.sh.orig	2017-10-27 02:08:53 UTC
2
+++ build/ld.bsd.gcc.sh
3
@@ -33,13 +33,8 @@ LD_REF_SYMBOLS="-Wl,-no-whole-archive"
4
 
5
 # build command
6
 DLIB_CMD="$LD -shared"
7
-
8
-#EXE_CMD="$LD -static-libstdc++ -static-libgcc"
9
-source "${0%exe.sh}exe_cmd.sh" # EXE_CMD is defined in build/ld.linux.exe_cmd.sh
10
-
11
-EXE_STATIC_CMD="$EXE_CMD"
12
-#EXE_CMD="$LD"
13
-#EXE_STATIC_CMD="$LD -static"
14
+EXE_CMD="$LD"
15
+EXE_STATIC_CMD="$LD -static"
16
 
17
 # versioned output
18
 if [ "$VERS" = "" ]
(-)biology/sra-tools/files/patch-build_ld.sh (+60 lines)
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1
--- build/ld.sh.orig	2017-10-27 02:08:53 UTC
2
+++ build/ld.sh
3
@@ -68,6 +68,8 @@ HAVE_M=0
4
 NEED_M=1
5
 HAVE_XML=0
6
 NEED_XML=0
7
+HAVE_MBEDTLS=0
8
+NEED_MBEDTLS=0
9
 HAVE_KFC=0
10
 HAVE_KAPP=0
11
 HAVE_NCBI_VDB=0
12
@@ -294,11 +296,12 @@ do
13
         LIBS="$LIBS $1"
14
         ;;
15
 
16
-    -[lds]ncbi-vdb)
17
+    -[lds]ncbi-vdb*)
18
         HAVE_NCBI_VDB=1
19
         KPROC=4
20
-        HAVE_GZIP=1
21
-        HAVE_BZIP=1
22
+        NEED_GZIP=1
23
+        NEED_BZIP=1
24
+	NEED_MBEDTLS=1
25
         HAVE_KFC=1
26
         NEED_M=1
27
 
28
@@ -310,18 +313,19 @@ do
29
     -[lds]ncbi-ngs-c++)
30
         HAVE_NCBI_VDB=1
31
         KPROC=4
32
-        HAVE_GZIP=1
33
-        HAVE_BZIP=1
34
+        NEED_GZIP=1
35
+        NEED_BZIP=1
36
         HAVE_KFC=1
37
         NEED_M=1
38
         NEED_XML=$CONFIGURE_FOUND_XML2
39
         LIBS="$LIBS $1"
40
         ;;
41
-    -[lds]ncbi-wvdb)
42
+    -[lds]ncbi-wvdb*)
43
         HAVE_NCBI_WVDB=1
44
         KPROC=4
45
-        HAVE_GZIP=1
46
-        HAVE_BZIP=1
47
+        NEED_GZIP=1
48
+        NEED_BZIP=1
49
+        NEED_MBEDTLS=1
50
         HAVE_KFC=1
51
         NEED_M=16
52
         NEED_XML=$CONFIGURE_FOUND_XML2
53
@@ -515,6 +519,7 @@ fi
54
 # supply missing libraries
55
 [ $HAVE_GZIP -eq 0 ] && [ $NEED_GZIP -ne 0 ] && LIBS="$LIBS -lz"
56
 [ $HAVE_BZIP -eq 0 ] && [ $NEED_BZIP -ne 0 ] && LIBS="$LIBS -lbz2"
57
+[ $HAVE_MBEDTLS -eq 0 ] && [ $NEED_MBEDTLS -ne 0 ] && LIBS="$LIBS -lmbedtls -lmbedcrypto -lmbedx509"
58
 [ $HAVE_DL -eq 0 ] && [ $NEED_DL -ne 0 ] && LIBS="$LIBS -ldl"
59
 [ $HAVE_M -eq 0 ] && [ $NEED_M -ne 0 ] && HAVE_M=16
60
 [ $HAVE_XML -eq 0 ] && [ $NEED_XML -ne 0 ] && HAVE_XML=32
(-)biology/sra-tools/files/patch-setup_konfigure.perl (+252 lines)
Line 0 Link Here
1
--- setup/konfigure.perl.orig	2017-08-03 16:17:04 UTC
2
+++ setup/konfigure.perl
3
@@ -186,7 +186,7 @@ if ($OPT{'help'}) {
4
 foreach (@ARGV) {
5
     @_ = split('=');
6
     next if ($#_ != 1);
7
-    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS');
8
+    $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS');
9
 }
10
 
11
 println "Configuring $PACKAGE_NAME package";
12
@@ -198,7 +198,7 @@ print "checking system type... " unless 
13
 my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
14
 println $OSTYPE unless ($AUTORUN);
15
 
16
-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
17
+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
18
     println "configure: error: unsupported system '$OSTYPE'";
19
     exit 1;
20
 }
21
@@ -213,7 +213,7 @@ if ($OS eq 'linux') {
22
 
23
 print "checking machine architecture... " unless ($AUTORUN);
24
 println $MARCH unless ($AUTORUN);
25
-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
26
+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i) {
27
     println "configure: error: unsupported architecture '$OSTYPE'";
28
     exit 1;
29
 }
30
@@ -298,7 +298,7 @@ print "checking for supported architectu
31
 
32
 my $BITS;
33
 
34
-if ($MARCH =~ /x86_64/i) {
35
+if ($MARCH =~ /(x86_|amd)64/i) {
36
     $BITS = 64;
37
 } elsif ($MARCH eq 'fat86') {
38
     $BITS = '32_64';
39
@@ -331,6 +331,18 @@ if ($OSTYPE =~ /linux/i) {
40
     $EXEX = '';
41
     $OSINC = 'unix';
42
     $TOOLS = 'clang' unless ($TOOLS);
43
+} elsif ($OSTYPE =~ /freebsd/i) {
44
+    $LPFX = 'lib';
45
+    $OBJX = 'o';
46
+    $LOBX = 'pic.o';
47
+    $LIBX = 'a';
48
+    $SHLX = 'so';
49
+    $EXEX = '';
50
+    $OSINC = 'unix';
51
+    unless ($TOOLS) {
52
+        $TOOLS = 'clang';
53
+        $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS});
54
+    }
55
 } elsif ($OSTYPE eq 'win') {
56
     $TOOLS = 'vc++';
57
 } else {
58
@@ -346,17 +358,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $M
59
 
60
 print "checking for supported tool chain... " unless ($AUTORUN);
61
 
62
+$CC      = $OPT{CC     } if ($OPT{CC     });
63
 $CPP     = $OPT{CXX    } if ($OPT{CXX    });
64
 $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS});
65
 
66
 if ($TOOLS =~ /gcc$/) {
67
     $CPP  = 'g++' unless ($CPP);
68
-    $CC   = "$TOOLS -c";
69
+    $CC   = 'gcc' unless ($CC);
70
+    $LD   = $CC;
71
+    $CC   = "$CC -c";
72
     $CP   = "$CPP -c";
73
     $AR   = 'ar rc';
74
     $ARX  = 'ar x';
75
     $ARLS = 'ar t';
76
-    $LD   = $TOOLS;
77
     $LP   = $CPP;
78
 
79
     $DBG = '-g -DDEBUG';
80
@@ -366,21 +380,24 @@ if ($TOOLS =~ /gcc$/) {
81
     $MD  = '-MD';
82
 } elsif ($TOOLS eq 'clang') {
83
     $CPP  = 'clang++' unless ($CPP);
84
-    $CC   = 'clang -c';
85
-    my $versionMin = '-mmacosx-version-min=10.6';
86
+    $CC   = 'clang' unless ($CC);
87
+    $LD   = $CC;
88
+    $CC   = "$CC -c";
89
+    my $versionMin = '';
90
+    $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i);
91
     $CP   = "$CPP -c $versionMin";
92
     if ($BITS ne '32_64') {
93
         $ARCH_FL = '-arch i386' if ($BITS == 32);
94
         $OPT = '-O3';
95
         $AR      = 'ar rc';
96
-        $LD      = "clang $ARCH_FL";
97
+        $LD      = "$LD $ARCH_FL";
98
         $LP      = "$CPP $versionMin $ARCH_FL";
99
     } else {
100
         $MAKE_MANIFEST = '( echo "$^" > $@/manifest )';
101
         $ARCH_FL       = '-arch i386 -arch x86_64';
102
         $OPT    = '-O3';
103
         $AR     = 'libtool -static -o';
104
-        $LD     = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
105
+        $LD     = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
106
         $LP     = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load";
107
     }
108
     $ARX  = 'ar x';
109
@@ -759,13 +776,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os
110
 # install paths
111
 EndText
112
 
113
-    L($F, "INST_BINDIR = $OPT{'bindir'}"      ) if ($OPT{'bindir'});
114
-    L($F, "INST_LIBDIR = $OPT{'libdir'}"      ) if ($OPT{'libdir'});
115
-    L($F, "INST_INCDIR = $OPT{'includedir'}"  ) if ($OPT{'includedir'});
116
-    L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'});
117
-    L($F, "INST_SHAREDIR = $OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
118
-    L($F, "INST_JARDIR = $OPT{'javadir'}"     ) if ($OPT{'javadir'});
119
-    L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'});
120
+    L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}"      ) if ($OPT{'bindir'});
121
+    L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}"      ) if ($OPT{'libdir'});
122
+    L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}"  ) if ($OPT{'includedir'});
123
+    L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'});
124
+    L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}"  ) if ($OPT{'sharedir'});
125
+    L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}"     ) if ($OPT{'javadir'});
126
+    L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'});
127
 
128
     my ($E_VERSION_SHLX, $VERSION_SHLX,
129
         $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX);
130
@@ -829,7 +846,7 @@ MAJMIN_EXEX  = \$(EXEX).\$(MAJMIN)
131
 MAJVERS_EXEX = \$(EXEX).\$(MAJVERS)
132
 
133
 # system architecture and wordsize
134
-ARCH = $ARCH
135
+override ARCH = $ARCH
136
 EndText
137
 
138
     L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH);
139
@@ -864,7 +881,7 @@ EndText
140
     }
141
     L($F, "PIC     = $PIC") if ($PIC);
142
     if ($PKG{LNG} eq 'C') {
143
-        if ($TOOLS =~ /clang/i) {
144
+        if ($OSTYPE =~ /darwin/i) {
145
    L($F, 'SONAME  = -install_name ' .
146
                '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
147
    L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
148
@@ -975,7 +992,7 @@ EndText
149
     L($F, '# directory rules');
150
     if ($PKG{LNG} eq 'C') {
151
         L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) '
152
-            . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):');
153
+            . '$(OBJDIR) $(INST_LIBDIR):');
154
         T($F, 'mkdir -p $@');
155
     } elsif ($PKG{LNG} eq 'JAVA') {
156
         # test if we have jni header path
157
@@ -1005,12 +1022,12 @@ EndText
158
     L($F, 'export CONFIGURE_FOUND_XML2');
159
     L($F);
160
 
161
-    if ($OS eq 'linux' || $OS eq 'mac') {
162
+    if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') {
163
         L($F, '# installation rules');
164
         L($F,
165
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
166
+        '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)');
167
         T($F, '@ echo -n "installing \'$(@F)\'... "');
168
-        T($F, '@ if cp $^ $@ && chmod 644 $@;                         \\');
169
+        T($F, '@ if $(BSD_INSTALL_DATA) $^ $@;                        \\');
170
         T($F, '  then                                                 \\');
171
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
172
                      . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) '
173
@@ -1019,7 +1036,7 @@ EndText
174
         T($F, '      ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) '
175
                       . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\');
176
         T($F, '      ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' .
177
-   '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
178
+   '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));'
179
                                                               . ' \\');
180
         T($F, '      echo success;                                    \\');
181
         T($F, '  else                                                 \\');
182
@@ -1029,15 +1046,15 @@ EndText
183
         L($F);
184
 
185
         L($F,
186
-        '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
187
+        '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)');
188
         T($F, '@ echo -n "installing \'$(@F)\'... "');
189
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
190
+        T($F, '@ if $(BSD_INSTALL_LIB) $^ $@;                         \\');
191
         T($F, '  then                                                 \\');
192
         if ($OS ne 'mac') {
193
           T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
194
                       . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@);    \\');
195
         }
196
-        if ($OS eq 'linux') {
197
+        if ($OS eq 'linux' || $OS eq 'bsd') {
198
           T($F, '      ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\');
199
         } elsif ($OS eq 'mac') {
200
           T($F, '      ln -sf $(@F) '
201
@@ -1056,7 +1073,7 @@ EndText
202
 
203
         L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)');
204
         T($F, '@ echo -n "installing \'$(@F)\'... "');
205
-        T($F, '@ if cp $^ $@ && chmod 755 $@;                         \\');
206
+        T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@;                     \\');
207
         T($F, '  then                                                 \\');
208
         T($F, '      rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) '
209
                       . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@);     \\');
210
@@ -1338,7 +1355,7 @@ sub find_in_dir {
211
                 ++$found;
212
             }
213
             if (! $found) {
214
-                my $libdir = File::Spec->catdir($dir, 'lib' . $BITS);
215
+                my $libdir = File::Spec->catdir($dir, 'lib');
216
                 my $f = File::Spec->catdir($libdir, $lib);
217
                 print "\tchecking $f\n\t" if ($OPT{'debug'});
218
                 if (-e $f) {
219
@@ -1480,12 +1497,12 @@ sub find_lib {
220
 
221
 sub check_compiler {
222
     my ($t, $n, $I, @l) = @_;
223
-    my $tool = $TOOLS;
224
+    my $tool = $CC;
225
 
226
     if ($t eq 'L') {
227
         print "checking for $n library... ";
228
     } elsif ($t eq 'O') {
229
-        if ($tool && ($tool =~ /gcc$/ || $tool =~ /g\+\+$/)) {
230
+        if ($tool && ($tool =~ /gcc/ || $tool =~ /g\+\+/)) {
231
             print "checking whether $tool accepts $n... ";
232
         } else {
233
             return;
234
@@ -1515,6 +1532,9 @@ sub check_compiler {
235
         } elsif ($n eq 'magic') {
236
             $library = '-lmagic';
237
             $log = '#include <magic.h> \n int main() { magic_open     (0); }\n'
238
+        } elsif ($n eq 'mbedtls') {
239
+            $library = '-lmbedtls';
240
+            $log = '#include <mbedtls/version.h> \n int main() { mbedtls_version_get_string(0); }\n'
241
         } elsif ($n eq 'xml2') {
242
             $library  = '-lxml2';
243
             $library .=       ' -liconv' if ($OS eq 'mac');
244
@@ -1551,7 +1571,7 @@ sub check_compiler {
245
             my $l = $l [ $i ];
246
             next if ( $l && ! -d $l );
247
             my $gcc = "| $tool -xc $flags " . ($I ? "-I$I " : ' ')
248
-                                      . ($l ? "-L$l " : ' ') . "- $library";
249
+                                      . ($l ? "-L$l " : ' ') . "-o a.out - $library";
250
             $gcc .= ' 2> /dev/null' unless ($OPT{'debug'});
251
 
252
             open GCC, $gcc or last;
(-)biology/sra-tools/files/patch-setup_os-arch.prl (+20 lines)
Line 0 Link Here
1
--- setup/os-arch.prl.orig	2017-08-03 16:17:04 UTC
2
+++ setup/os-arch.prl
3
@@ -11,6 +11,8 @@ sub OsArch {
4
         chomp $UNAME;
5
         if ($UNAME =~ /Darwin/) {
6
             $HOST_OS = 'mac';
7
+        } elsif ($UNAME =~ /.*BSD/) {
8
+            $HOST_OS = 'bsd';
9
         } elsif ($UNAME =~ /Linux/) {
10
             $HOST_OS = 'linux';
11
         } elsif ($UNAME =~ /SunOS/) {
12
@@ -49,6 +51,8 @@ sub OsArch {
13
                 }
14
             } elsif ($MARCH =~ /x86_64/) {
15
                 $HOST_ARCH = 'x86_64';
16
+            } elsif ($MARCH =~ /amd64/) {
17
+                $HOST_ARCH = 'x86_64';
18
             } elsif ($MARCH =~ /i86pc/) {
19
                 $HOST_ARCH = 'x86_64';
20
                 @ARCHITECTURES = qw(x86_64 i386);
(-)biology/sra-tools/files/patch-setup_package.prl (+26 lines)
Line 0 Link Here
1
--- setup/package.prl.orig	2017-08-03 16:17:04 UTC
2
+++ setup/package.prl
3
@@ -12,6 +12,7 @@ sub PKG { ( LNG   => 'C',
4
 sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include'        , },
5
                 { name => 'hdf5' , Include => '/usr/include'        , },
6
                 { name => 'magic', Include => '/usr/include'        , },
7
+                { name => 'mbedtls', Include => '/usr/include'        , },
8
                 { name => 'xml2' , Include => '/usr/include/libxml2', } ) }
9
 sub REQ { (
10
             { name    => 'ngs-sdk',
11
@@ -58,6 +59,15 @@ sub REQ { (
12
               origin  => 'E',
13
               type    => 'LIO',
14
             },
15
+            { name    => 'mbedtls',
16
+              option  => 'with-mbedtls-prefix',
17
+              origin  => 'E',
18
+              type    => 'LIO',
19
+              pkgpath => '/usr',
20
+              usrpath => '$HOME',
21
+              include => 'mbedtls/config.h',
22
+              lib     => 'libmbedtls.so',
23
+            },
24
             { name    => 'xml2',
25
               option  => 'with-xml2-prefix',
26
               origin  => 'E',
(-)biology/sra-tools/files/patch-test_general-loader_VDB-3250_prepare__test__data.sh (+11 lines)
Line 0 Link Here
1
--- test/general-loader/VDB-3250/prepare_test_data.sh.orig	2017-10-27 02:08:53 UTC
2
+++ test/general-loader/VDB-3250/prepare_test_data.sh
3
@@ -160,7 +160,7 @@ test_check_exe LOADER_EXE $BIN_DIR/gener
4
 #
5
 cd $TEST_DATA_DIR
6
 
7
-_exec make
8
+_exec gmake
9
 
10
 test_check_exe PREPARER_EXE $TEST_BIN_DIR/prepare_test_data
11
 test_check_exe CHECKER_EXE $TEST_BIN_DIR/check_test_result
(-)biology/sra-tools/files/patch-test_kar_kar-test.sh (+22 lines)
Line 0 Link Here
1
--- test/kar/kar-test.sh.orig	2017-10-27 02:08:53 UTC
2
+++ test/kar/kar-test.sh
3
@@ -38,6 +38,10 @@ case $UNAME in
4
     (Linux)
5
         OS=linux
6
         ;;
7
+    (FreeBSD)
8
+        OS=bsd
9
+        MD5TOOL=/sbin/md5
10
+        ;;
11
     (Darwin)
12
         OS=mac
13
         MD5TOOL=/sbin/md5
14
@@ -129,7 +133,7 @@ test_create_options ()
15
                     exit 1
16
                 fi
17
                 ;;
18
-            (Darwin)
19
+            (Darwin|FreeBSD)
20
                 if [ ! -x $MD5TOOL ]
21
                 then
22
                     echo "could not locate executable md5 tool"
(-)biology/sra-tools/files/patch-tools_bam-loader_loader-imp.c (+10 lines)
Line 0 Link Here
1
--- tools/bam-loader/loader-imp.c.orig	2017-08-03 16:17:04 UTC
2
+++ tools/bam-loader/loader-imp.c
3
@@ -73,6 +73,7 @@
4
 
5
 #include <unistd.h>
6
 #include <fcntl.h>
7
+#include <sys/stat.h>
8
 #include <sys/mman.h>
9
 #include <stdlib.h>
10
 #include <stdio.h>
(-)biology/sra-tools/files/patch-tools_copycat_Makefile (+11 lines)
Line 0 Link Here
1
--- tools/copycat/Makefile.orig	2017-08-03 16:17:04 UTC
2
+++ tools/copycat/Makefile
3
@@ -92,7 +92,7 @@ COPYCAT_LIB = \
4
 	-stk-version \
5
 	-sncbi-vdb \
6
 	-skff \
7
-	-smagic-static
8
+	-smagic
9
 
10
 
11
 $(BINDIR)/copycat: $(COPYCAT_OBJ)
(-)biology/sra-tools/files/patch-tools_copycat_ccfileformat.c (+19 lines)
Line 0 Link Here
1
--- tools/copycat/ccfileformat.c.orig	2017-08-03 16:17:04 UTC
2
+++ tools/copycat/ccfileformat.c
3
@@ -184,11 +184,11 @@ rc_t CCFileFormatMake (CCFileFormat ** p
4
             KConfigRelease ( kfg );
5
             if ( rc == 0 )
6
             {
7
-                char magicpath[1024];
8
-                size_t num_writ;
9
-                rc = string_printf ( magicpath, sizeof ( magicpath ), &num_writ, "%S/magic", bindir );
10
-                StringWhack ( bindir );
11
-                if ( rc == 0 )
12
+//                char magicpath[1024];
13
+//                size_t num_writ;
14
+//                rc = string_printf ( magicpath, sizeof ( magicpath ), &num_writ, "%S/magic", bindir );
15
+//                StringWhack ( bindir );
16
+//                if ( rc == 0 )
17
                 {
18
                     rc = KExtFileFormatMake (&self->ext, exttable, sizeof (exttable) - 1,
19
                                              formattable, sizeof (formattable) - 1);
(-)biology/sra-tools/files/patch-tools_fastq-loader_common-writer.c (+10 lines)
Line 0 Link Here
1
--- tools/fastq-loader/common-writer.c.orig	2017-08-03 16:17:04 UTC
2
+++ tools/fastq-loader/common-writer.c
3
@@ -58,6 +58,7 @@
4
 
5
 #include <unistd.h>
6
 #include <fcntl.h>
7
+#include <sys/stat.h>
8
 #include <sys/mman.h>
9
 
10
 #define USE_READER_THREAD (1)
(-)biology/sra-tools/files/patch-tools_general-loader_gw-dumper.cpp (+10 lines)
Line 0 Link Here
1
--- tools/general-loader/gw-dumper.cpp.orig	2017-08-03 16:17:04 UTC
2
+++ tools/general-loader/gw-dumper.cpp
3
@@ -34,7 +34,6 @@
4
 
5
 #include <stdio.h>
6
 #include <string.h>
7
-#include <byteswap.h>
8
 #include <stdlib.h>
9
 #include <stdint.h>
10
 
(-)biology/sra-tools/files/patch-tools_pacbio-load_Makefile (+11 lines)
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1
--- tools/pacbio-load/Makefile.orig	2017-08-03 16:17:04 UTC
2
+++ tools/pacbio-load/Makefile
3
@@ -105,7 +105,7 @@ PACBIO_LOAD_LIB = \
4
 	-stk-version \
5
 	-skdf5 \
6
 	-sload \
7
-	-shdf5 \
8
+	-lhdf5 \
9
 	-sncbi-wvdb \
10
 	-sm \
11
 
(-)biology/sra-tools/files/patch-tools_vdb-decrypt_Makefile (+11 lines)
Line 0 Link Here
1
--- tools/vdb-decrypt/Makefile.orig	2017-08-03 16:17:04 UTC
2
+++ tools/vdb-decrypt/Makefile
3
@@ -25,7 +25,7 @@
4
 
5
 default: std
6
 
7
-USE_GCC_IF_ICC = 1
8
+#USE_GCC_IF_ICC = 1
9
 
10
 TOP ?= $(abspath ../..)
11
 MODULE = tools/vdb-decrypt
(-)biology/sra-tools/pkg-descr (+18 lines)
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1
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.
2
3
SRAs operated by International Nucleotide Sequence Database Collaboration
4
houses sequence reads and alignments generated by "next-gen" sequencers.
5
SRA tools allows conversion of .sra files, which INSDC SRAs maintain,
6
from/to other formats that the 'next-gen' sequenecers generate including:
7
8
* csfasta/csqual (ABI SOLiD)
9
* fastq (and fasta for writing)
10
* hdf5 (PacBio, reading only)
11
* qseq (older Illumina)
12
* sam (writing only) / bam (reading only)
13
* sff
14
15
The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data
16
and local SRA files.
17
18
WWW: https://github.com/ncbi/sra-tools/wiki
(-)biology/sra-tools/pkg-plist (+41 lines)
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1
bin/abi-dump
2
bin/abi-load
3
bin/align-info
4
bin/bam-load
5
bin/cache-mgr
6
bin/cg-load
7
bin/copycat
8
bin/fastdump
9
bin/fastq-dump
10
bin/fastq-load
11
bin/helicos-load
12
bin/illumina-dump
13
bin/illumina-load
14
bin/kar
15
bin/kdbmeta
16
bin/latf-load
17
bin/pacbio-load
18
bin/prefetch
19
bin/rcexplain
20
bin/sam-dump
21
bin/sff-dump
22
bin/sff-load
23
bin/sra-pileup
24
bin/sra-sort
25
bin/sra-stat
26
bin/srapath
27
bin/srf-load
28
bin/test-sra
29
bin/vdb-config
30
bin/vdb-copy
31
bin/vdb-decrypt
32
bin/vdb-dump
33
bin/vdb-encrypt
34
bin/vdb-get
35
bin/vdb-lock
36
bin/vdb-passwd
37
bin/vdb-unlock
38
bin/vdb-validate
39
etc/ncbi/certs.kfg
40
etc/ncbi/default.kfg
41
etc/ncbi/vdb-copy.kfg

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