sra-tools: Clean up

Patch out @rpath
Fully remove Java references
Remove remaining cruft from fbsd2pkg conversion

diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 142b41bcf1944250cfd1845ecd7462116cebe750..b2441eadeca164b2e08618e1e4faca9f2641f464 100644 (file)
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -5,14 +5,6 @@
 #              Sat Aug 12 11:25:27 CDT 2023               #
 ###########################################################
 
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#LICENSE_COMB=         multi
-#LICENSE_FILE_PD=      ${WRKSRC}/LICENSE
-#LICENSE_DISTFILES_LGPL21+ =
-#USE_LDCONFIG=         ${PREFIX}/lib64
-
 DISTNAME=              sra-tools-3.0.6
 CATEGORIES=            biology
 MASTER_SITES=          ${MASTER_SITE_GITHUB:=outpaddling/}
@@ -22,11 +14,7 @@ GITHUB_SUBMODULES+=  outpaddling ncbi-vdb 802ae6e ncbi-vdb
 OWNER=         bacon@NetBSD.org
 HOMEPAGE=      https://github.com/ncbi/sra-tools
 COMMENT=       NCBI's toolkit for handling data in INSDC Sequence Read Archives
-# Check this
-LICENSE=       public-domain
-
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=      no
+LICENSE=       public-domain AND gnu-lgpl-v2.1
 
 # Upstream explicitly supports specific platforms
 # Untested on other platforms, aarch64 support was recently added upstream
@@ -34,9 +22,6 @@ ONLY_FOR_PLATFORM=    *-*-aarch64 *-*-x86_64
 
 USE_LANGUAGES= c c++
 USE_TOOLS+=    bash bison cmake
-# USE_JAVA=    yes
-# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
-# USE_JAVA2=   17
 
 # The config.c and file-path.posix.cpp reinplaces follow
 # static patches.  Run "make clean patch" before updating
@@ -56,13 +41,14 @@ SUBST_STAGE.submoddir=      pre-configure
 SUBST_SED.submoddir+=  -e 's|/../ncbi-vdb|/ncbi-vdb|g'
 SUBST_FILES.submoddir+=        CMakeLists.txt
 
-# FreeBSD's SHEBANG_FILES may include bash, perl, python, etc.
-# I don't know which is which, so you'll have to finish.
-# Add bash, etc. to USE_TOOLS if used below.
-REPLACE_BASH=  */*.sh */*/*.sh */*/*/*.sh
+SUBST_CLASSES+=                srarpath
+SUBST_STAGE.srarpath=  post-configure
+SUBST_SED.srarpath+=   -e 's|@rpath|${PREFIX}/lib|g'
+SUBST_FILES.srarpath+= cmake-pkgsrc-build/ngs/ngs-sdk/CMakeFiles/*/link.txt
+
+REPLACE_BASH=  */*.sh */*/*.sh */*/*/*.sh */*/*/*/*.sh
 
 USE_CMAKE=     yes
-# Check this
 CMAKE_ARGS+=   -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
 CMAKE_ARGS+=   -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 BUILDLINK_TRANSFORM.NetBSD+=   rm:-ldl # ncbi-vdb/CMakeLists.posix.txt
@@ -71,12 +57,19 @@ EXAMPLESDIR=        ${PREFIX}/share/examples/sra-tools
 
 .include "../../mk/bsd.prefs.mk"
 
-# FIXME: Check for libstdc++-static on Linux
 pre-configure:
 .if ${OPSYS} == NetBSD
+       # Incorrect code found before bsd/byteswap.h
+       #ifndef __NetBSD__ doesn't help
        ${RM} ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64/byteswap.h
 .endif
-       cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON .. && make
+       cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
+       # Unsure how to prevent cmake from generating @rpath in the first place
+       # No instances of @rpath or -install_name in any files before configure
+       for f in ${WRKSRC}/ncbi-vdb/build/libs/ncbi-vdb/CMakeFiles/*/link.txt; do \
+               ${SED} -e 's|@rpath|${PREFIX}/lib|g' $${f} > $${f}.tmp && ${MV} -f $${f}.tmp $${f}; \
+       done
+       cd ${WRKSRC}/ncbi-vdb/build && ${MAKE}
 
 post-install:
        ${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION_NOREV}
@@ -95,16 +88,11 @@ post-install:
 .include "../../devel/libepoll-shim/buildlink3.mk"
 .endif
 
-# Triggers openjdk install on Linux even if installed via Yum
-# FIXME: Should we just build without Java to avoid these issues?
-# .if ${OPSYS} == NetBSD
-# .include "../../mk/java-vm.mk"
-# .endif
 .include "../../mk/pthread.buildlink3.mk"
 .include "../../devel/cmake/build.mk"
 .include "../../textproc/libxml2/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/zstd/buildlink3.mk"
-# FIXME: cmake is not finding this
+# FIXME: cmake is not actually finding this
 .include "../../security/mbedtls/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"