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sra-tools: Switch from fork to NCBI engineering branch 

Upstream has merged my BSD patches, so this package will
be much easier to maintain from now on
master
Jason W. Bacon 2024-03-21 17:41:41 -05:00
parent 614f88aa48
commit af8d81afc2
4 changed files with 67 additions and 51 deletions
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12
sra-tools/Makefile
View File

@ -1,10 +1,10 @@
# $NetBSD$
DISTNAME= sra-tools-3.0.6
DISTNAME= sra-tools-3.0.10.133
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
GITHUB_TAG= 984f1493e8612cd59a269569bf8c06e25e4e604c
GITHUB_SUBMODULES+= outpaddling ncbi-vdb 38972fc ncbi-vdb
MASTER_SITES= ${MASTER_SITE_GITHUB:=ncbi/}
GITHUB_TAG= 2a26be56758d6d6be3362f8c229f09ced4530873
GITHUB_SUBMODULES+= ncbi ncbi-vdb ff143ec1 ncbi-vdb
OWNER= bacon@NetBSD.org
HOMEPAGE= https://github.com/ncbi/sra-tools
@ -27,7 +27,7 @@ SUBST_FILES.etcdir+= ncbi-vdb/libs/kfg/config.c
SUBST_CLASSES+= binpath
SUBST_STAGE.binpath= pre-configure
SUBST_SED.binpath+= -e 's|/usr/local/bin|${PREFIX}/bin|g'
SUBST_SED.binpath+= -e 's|/usr/local|${PREFIX}|g'
SUBST_FILES.binpath+= tools/external/driver-tool/file-path.posix.cpp
SUBST_CLASSES+= submoddir
@ -70,7 +70,7 @@ pre-configure:
cd ${WRKSRC}/ncbi-vdb/build && ${MAKE}
post-install:
${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION_NOREV}
${STRIP} ${DESTDIR}${PREFIX}/bin/*.3.1.0
${MV} ${DESTDIR}${PREFIX}/share/examples ${DESTDIR}${PREFIX}/share/examples-sratools
${MKDIR} ${DESTDIR}${EXAMPLESDIR}
${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}

79
sra-tools/PLIST
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@ -1,92 +1,92 @@
@comment $NetBSD$
bin/abi-dump
bin/abi-dump.3
bin/abi-dump.${PKGVERSION}
bin/abi-dump.3.1.0
bin/align-info
bin/align-info.3
bin/align-info.${PKGVERSION}
bin/align-info.3.1.0
bin/cache-mgr
bin/cache-mgr.3
bin/cache-mgr.${PKGVERSION}
bin/cache-mgr.3.1.0
bin/check-corrupt
bin/check-corrupt.3
bin/check-corrupt.${PKGVERSION}
bin/check-corrupt.3.1.0
bin/fasterq-dump
bin/fasterq-dump-orig.${PKGVERSION}
bin/fasterq-dump-orig.3.1.0
bin/fasterq-dump.3
bin/fasterq-dump.${PKGVERSION}
bin/fasterq-dump.3.1.0
bin/fastq-dump
bin/fastq-dump-orig.${PKGVERSION}
bin/fastq-dump-orig.3.1.0
bin/fastq-dump.3
bin/fastq-dump.${PKGVERSION}
bin/fastq-dump.3.1.0
bin/illumina-dump
bin/illumina-dump.3
bin/illumina-dump.${PKGVERSION}
bin/illumina-dump.3.1.0
bin/kdbmeta
bin/kdbmeta.3
bin/kdbmeta.${PKGVERSION}
bin/kdbmeta.3.1.0
bin/ngs-pileup
bin/ngs-pileup.3
bin/ngs-pileup.${PKGVERSION}
bin/ngs-pileup.3.1.0
bin/prefetch
bin/prefetch-orig.${PKGVERSION}
bin/prefetch-orig.3.1.0
bin/prefetch.3
bin/prefetch.${PKGVERSION}
bin/prefetch.3.1.0
bin/rcexplain
bin/rcexplain.3
bin/rcexplain.${PKGVERSION}
bin/rcexplain.3.1.0
bin/ref-variation
bin/ref-variation.3
bin/ref-variation.${PKGVERSION}
bin/ref-variation.3.1.0
bin/sam-dump
bin/sam-dump-orig.${PKGVERSION}
bin/sam-dump-orig.3.1.0
bin/sam-dump.3
bin/sam-dump.${PKGVERSION}
bin/sam-dump.3.1.0
bin/sff-dump
bin/sff-dump.3
bin/sff-dump.${PKGVERSION}
bin/sff-dump.3.1.0
bin/sra-info
bin/sra-info.3
bin/sra-info.${PKGVERSION}
bin/sra-info.3.1.0
bin/sra-pileup
bin/sra-pileup-orig.${PKGVERSION}
bin/sra-pileup-orig.3.1.0
bin/sra-pileup.3
bin/sra-pileup.${PKGVERSION}
bin/sra-pileup.3.1.0
bin/sra-search
bin/sra-search.3
bin/sra-search.${PKGVERSION}
bin/sra-search.3.1.0
bin/sra-stat
bin/sra-stat.3
bin/sra-stat.${PKGVERSION}
bin/sra-stat.3.1.0
bin/srapath
bin/srapath-orig.${PKGVERSION}
bin/srapath-orig.3.1.0
bin/srapath.3
bin/srapath.${PKGVERSION}
bin/srapath.3.1.0
bin/sratools
bin/sratools.3
bin/sratools.${PKGVERSION}
bin/sratools.3.1.0
bin/test-sra
bin/test-sra.3
bin/test-sra.${PKGVERSION}
bin/test-sra.3.1.0
bin/var-expand
bin/var-expand.3
bin/var-expand.${PKGVERSION}
bin/var-expand.3.1.0
bin/vdb-config
bin/vdb-config.3
bin/vdb-config.${PKGVERSION}
bin/vdb-config.3.1.0
bin/vdb-decrypt
bin/vdb-decrypt.3
bin/vdb-decrypt.${PKGVERSION}
bin/vdb-decrypt.3.1.0
bin/vdb-dump
bin/vdb-dump-orig.${PKGVERSION}
bin/vdb-dump-orig.3.1.0
bin/vdb-dump.3
bin/vdb-dump.${PKGVERSION}
bin/vdb-dump.3.1.0
bin/vdb-encrypt
bin/vdb-encrypt.3
bin/vdb-encrypt.${PKGVERSION}
bin/vdb-encrypt.3.1.0
bin/vdb-validate
bin/vdb-validate.3
bin/vdb-validate.${PKGVERSION}
bin/vdb-validate.3.1.0
include/ncbi-vdb/NGS.hpp
include/ngs/Alignment.hpp
include/ngs/AlignmentIterator.hpp
@ -181,21 +181,21 @@ include/ngs/win/stdbool.h
lib/libncbi-ngs-c++-static.a
lib/libncbi-ngs-c++.a
lib/libncbi-ngs-c++.a.3
lib/libncbi-ngs-c++.a.${PKGVERSION}
lib/libncbi-ngs-c++.a.3.1.0
lib/libncbi-ngs-static.a
lib/libncbi-ngs.a
lib/libncbi-ngs.a.3
lib/libncbi-ngs.a.${PKGVERSION}
lib/libncbi-ngs.a.3.1.0
lib/libncbi-ngs.so
lib/libncbi-ngs.so.3
lib/libncbi-ngs.so.${PKGVERSION}
lib/libncbi-ngs.so.3.1.0
lib/libngs-c++-static.a
lib/libngs-c++.a
lib/libngs-c++.a.3
lib/libngs-c++.a.${PKGVERSION}
lib/libngs-c++.a.3.1.0
lib/libngs-c++.so
lib/libngs-c++.so.3
lib/libngs-c++.so.${PKGVERSION}
lib/libngs-c++.so.3.1.0
share/examples/sra-tools/AlignSliceTest.cpp
share/examples/sra-tools/AlignTest.cpp
share/examples/sra-tools/DumpReferenceFASTA.cpp
@ -213,3 +213,4 @@ share/examples/sra-tools/python/PileupTest.py
share/examples/sra-tools/python/README.txt
share/examples/sra-tools/python/RefTest.py
share/examples/sra-tools/python/expected.txt

13
sra-tools/distinfo
View File

@ -1,12 +1,13 @@
$NetBSD$
BLAKE2s (outpaddling-ncbi-vdb-38972fc.tar.gz) = 600ac8ff4f2fbea9d2f06edc0277087e1559636226756eae415826dfbdb1fb5a
SHA512 (outpaddling-ncbi-vdb-38972fc.tar.gz) = 0cda01bf2faf59aa16c4a402bcc132d4a2fc948240f6e13b2f1d3d93c4f900a837ebf8c24ee8089e88ed4de90a8ab441a4176f8193052fd7b538e27384bcb118
Size (outpaddling-ncbi-vdb-38972fc.tar.gz) = 18978410 bytes
BLAKE2s (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 2a13546011d4ea0a000a7e1e5fdfdf1d915b6adbac8fd818967ebf4c1670dba5
SHA512 (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 9b1e671c92ba1006392160258c5b6fba85ba7dba59a23e9ed8b534ca31b46ed9e6cf2c92ea69dc2897f5a4aa9da31f5c8981cebb442236d11bcef76b854dbec9
Size (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 44961381 bytes
BLAKE2s (ncbi-ncbi-vdb-ff143ec1.tar.gz) = 66163ec0c658d03ed085425448ebbfebe23a67d28776d928384cdeb39d1bb4d1
SHA512 (ncbi-ncbi-vdb-ff143ec1.tar.gz) = bf35ad78623f90fd8f9ddf30f33c8b8febb44a40fee1abad215fd8f1a986725593a2c94c7da82b5b8362fe9308cbf3ee026d14eb9921dac2e090a7710b93d202
Size (ncbi-ncbi-vdb-ff143ec1.tar.gz) = 19057498 bytes
BLAKE2s (sra-tools-3.0.10.133-2a26be56758d6d6be3362f8c229f09ced4530873.tar.gz) = 5a0f368e997114b00fd38c9bd05bc1d01565bb14e46a85e007f1535b0501b799
SHA512 (sra-tools-3.0.10.133-2a26be56758d6d6be3362f8c229f09ced4530873.tar.gz) = f39bdd5036de1a1afec8c36badd5193ce4ce106202638f8e16e05518394c19241935aa6d8537d6554637663828ca44caaffd93f4ecbe0b731af67de7e868edce
Size (sra-tools-3.0.10.133-2a26be56758d6d6be3362f8c229f09ced4530873.tar.gz) = 45451112 bytes
SHA1 (patch-build_env.cmake) = 14add56e66e5578fd0d51ce55329285e0981ac4e
SHA1 (patch-ncbi-vdb_libs_kdbtext_path.hpp) = 78ec06ed7aa60fd2bded6129ddf25172c104ad77
SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
SHA1 (patch-tools_external_driver-tool_sratools.cpp) = c490d83f03471e6e8e34b8e88534469ed45b2886

14
sra-tools/patches/patch-ncbi-vdb_libs_kdbtext_path.hpp Normal file
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@ -0,0 +1,14 @@
$NetBSD$
# va_list
--- ncbi-vdb/libs/kdbtext/path.hpp.orig 2024-03-21 22:06:49.815904250 +0000
+++ ncbi-vdb/libs/kdbtext/path.hpp
@@ -28,6 +28,7 @@
#include <string>
#include <queue>
+#include <cstdarg>
#include <klib/rc.h>