/
Makefile
66 lines (52 loc) · 2.1 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
PORTNAME= sra-tools
DISTVERSION= 3.0.6
CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org
COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives
WWW= https://github.com/ncbi/sra-tools
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
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
USES= bison cmake shebangfix
USE_GITHUB= yes
USE_LDCONFIG= ${PREFIX}/lib64
USE_JAVA= yes
# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
JAVA_VERSION= 17+
OPTIONS_DEFINE= EXAMPLES
SHEBANG_GLOB= *.sh
GH_ACCOUNT= ncbi
GH_TUPLE+= ncbi:ncbi-vdb:${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' \
${WRKSRC}/ncbi-vdb/libs/kfg/config.c
${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
post-stage:
${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools
${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR}
${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools
${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java
${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python
post-stage-EXAMPLES-off:
${RM} -r ${STAGEDIR}${EXAMPLESDIR}
.include <bsd.port.mk>