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biology/sra-tools: Update to 3.2.1

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Fix fasterq-dump mkdir error:
https://github.com/ncbi/sra-tools/issues/1016#issuecomment-2737694569
Numerous other fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2025-03-21 06:27:22 -05:00
parent 75d4fc2a7e
commit a57f4b8dea
3 changed files with 47 additions and 45 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
biology/sra-tools/Makefile
View file

@ -1,5 +1,5 @@
PORTNAME= sra-tools PORTNAME= sra-tools
DISTVERSION= 3.2.0 DISTVERSION= 3.2.1
CATEGORIES= biology java CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org MAINTAINER= jwb@FreeBSD.org
@ -36,6 +36,8 @@ GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
PLIST_SUB= PORTVERSION=${PORTVERSION}
pre-configure: pre-configure:
# Reinplaces may follow static patches. Run "make clean patch" # Reinplaces may follow static patches. Run "make clean patch"
# before updating those patches so reinplaces do not get added to them. # before updating those patches so reinplaces do not get added to them.

10
biology/sra-tools/distinfo
View file

@ -1,5 +1,5 @@
TIMESTAMP = 1738157203 TIMESTAMP = 1742507022
SHA256 (ncbi-sra-tools-3.2.0_GH0.tar.gz) = 5ed9d0a61aa72c55566fb80b8b9293ad9006f528e7e11cba875d9377a0fc7b09 SHA256 (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 2558683c217ad2318833ab7731939617ed91dc79a6b1dee92bf88b56a1dc142a
SIZE (ncbi-sra-tools-3.2.0_GH0.tar.gz) = 60313243 SIZE (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 66684089
SHA256 (ncbi-ncbi-vdb-3.2.0_GH0.tar.gz) = 49fea92d9ec5ab38a5c06d1bcb057d1e7c9d4d39adcb7f31a3485ecc35bd5b77 SHA256 (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 535511984928ec5bac02a61fc6b4d1ca72a5b69c742f4882eabd32ed3a97621c
SIZE (ncbi-ncbi-vdb-3.2.0_GH0.tar.gz) = 19061110 SIZE (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 19061776

78
biology/sra-tools/pkg-plist
View file

@ -1,91 +1,91 @@
bin/abi-dump bin/abi-dump
bin/abi-dump.3 bin/abi-dump.3
bin/abi-dump.3.2.0 bin/abi-dump.%%PORTVERSION%%
bin/align-info bin/align-info
bin/align-info.3 bin/align-info.3
bin/align-info.3.2.0 bin/align-info.%%PORTVERSION%%
bin/cache-mgr bin/cache-mgr
bin/cache-mgr.3 bin/cache-mgr.3
bin/cache-mgr.3.2.0 bin/cache-mgr.%%PORTVERSION%%
bin/check-corrupt bin/check-corrupt
bin/check-corrupt.3 bin/check-corrupt.3
bin/check-corrupt.3.2.0 bin/check-corrupt.%%PORTVERSION%%
bin/fasterq-dump bin/fasterq-dump
bin/fasterq-dump-orig.3.2.0 bin/fasterq-dump-orig.%%PORTVERSION%%
bin/fasterq-dump.3 bin/fasterq-dump.3
bin/fasterq-dump.3.2.0 bin/fasterq-dump.%%PORTVERSION%%
bin/fastq-dump bin/fastq-dump
bin/fastq-dump-orig.3.2.0 bin/fastq-dump-orig.%%PORTVERSION%%
bin/fastq-dump.3 bin/fastq-dump.3
bin/fastq-dump.3.2.0 bin/fastq-dump.%%PORTVERSION%%
bin/illumina-dump bin/illumina-dump
bin/illumina-dump.3 bin/illumina-dump.3
bin/illumina-dump.3.2.0 bin/illumina-dump.%%PORTVERSION%%
bin/kdbmeta bin/kdbmeta
bin/kdbmeta.3 bin/kdbmeta.3
bin/kdbmeta.3.2.0 bin/kdbmeta.%%PORTVERSION%%
bin/ngs-pileup bin/ngs-pileup
bin/ngs-pileup.3 bin/ngs-pileup.3
bin/ngs-pileup.3.2.0 bin/ngs-pileup.%%PORTVERSION%%
bin/prefetch bin/prefetch
bin/prefetch-orig.3.2.0 bin/prefetch-orig.%%PORTVERSION%%
bin/prefetch.3 bin/prefetch.3
bin/prefetch.3.2.0 bin/prefetch.%%PORTVERSION%%
bin/rcexplain bin/rcexplain
bin/rcexplain.3 bin/rcexplain.3
bin/rcexplain.3.2.0 bin/rcexplain.%%PORTVERSION%%
bin/ref-variation bin/ref-variation
bin/ref-variation.3 bin/ref-variation.3
bin/ref-variation.3.2.0 bin/ref-variation.%%PORTVERSION%%
bin/sam-dump bin/sam-dump
bin/sam-dump-orig.3.2.0 bin/sam-dump-orig.%%PORTVERSION%%
bin/sam-dump.3 bin/sam-dump.3
bin/sam-dump.3.2.0 bin/sam-dump.%%PORTVERSION%%
bin/sff-dump bin/sff-dump
bin/sff-dump.3 bin/sff-dump.3
bin/sff-dump.3.2.0 bin/sff-dump.%%PORTVERSION%%
bin/sra-info bin/sra-info
bin/sra-info.3 bin/sra-info.3
bin/sra-info.3.2.0 bin/sra-info.%%PORTVERSION%%
bin/sra-pileup bin/sra-pileup
bin/sra-pileup-orig.3.2.0 bin/sra-pileup-orig.%%PORTVERSION%%
bin/sra-pileup.3 bin/sra-pileup.3
bin/sra-pileup.3.2.0 bin/sra-pileup.%%PORTVERSION%%
bin/sra-search bin/sra-search
bin/sra-search.3 bin/sra-search.3
bin/sra-search.3.2.0 bin/sra-search.%%PORTVERSION%%
bin/sra-stat bin/sra-stat
bin/sra-stat.3 bin/sra-stat.3
bin/sra-stat.3.2.0 bin/sra-stat.%%PORTVERSION%%
bin/srapath bin/srapath
bin/srapath-orig.3.2.0 bin/srapath-orig.%%PORTVERSION%%
bin/srapath.3 bin/srapath.3
bin/srapath.3.2.0 bin/srapath.%%PORTVERSION%%
bin/sratools bin/sratools
bin/sratools.3 bin/sratools.3
bin/sratools.3.2.0 bin/sratools.%%PORTVERSION%%
bin/test-sra bin/test-sra
bin/test-sra.3 bin/test-sra.3
bin/test-sra.3.2.0 bin/test-sra.%%PORTVERSION%%
bin/var-expand bin/var-expand
bin/var-expand.3 bin/var-expand.3
bin/var-expand.3.2.0 bin/var-expand.%%PORTVERSION%%
bin/vdb-config bin/vdb-config
bin/vdb-config.3 bin/vdb-config.3
bin/vdb-config.3.2.0 bin/vdb-config.%%PORTVERSION%%
bin/vdb-decrypt bin/vdb-decrypt
bin/vdb-decrypt.3 bin/vdb-decrypt.3
bin/vdb-decrypt.3.2.0 bin/vdb-decrypt.%%PORTVERSION%%
bin/vdb-dump bin/vdb-dump
bin/vdb-dump-orig.3.2.0 bin/vdb-dump-orig.%%PORTVERSION%%
bin/vdb-dump.3 bin/vdb-dump.3
bin/vdb-dump.3.2.0 bin/vdb-dump.%%PORTVERSION%%
bin/vdb-encrypt bin/vdb-encrypt
bin/vdb-encrypt.3 bin/vdb-encrypt.3
bin/vdb-encrypt.3.2.0 bin/vdb-encrypt.%%PORTVERSION%%
bin/vdb-validate bin/vdb-validate
bin/vdb-validate.3 bin/vdb-validate.3
bin/vdb-validate.3.2.0 bin/vdb-validate.%%PORTVERSION%%
include/ncbi-vdb/NGS.hpp include/ncbi-vdb/NGS.hpp
include/ngs/Alignment.hpp include/ngs/Alignment.hpp
include/ngs/AlignmentIterator.hpp include/ngs/AlignmentIterator.hpp
@ -184,21 +184,21 @@ jar/ngs-src.jar
lib64/libncbi-ngs-c++-static.a lib64/libncbi-ngs-c++-static.a
lib64/libncbi-ngs-c++.a lib64/libncbi-ngs-c++.a
lib64/libncbi-ngs-c++.a.3 lib64/libncbi-ngs-c++.a.3
lib64/libncbi-ngs-c++.a.3.2.0 lib64/libncbi-ngs-c++.a.%%PORTVERSION%%
lib64/libncbi-ngs-static.a lib64/libncbi-ngs-static.a
lib64/libncbi-ngs.a lib64/libncbi-ngs.a
lib64/libncbi-ngs.a.3 lib64/libncbi-ngs.a.3
lib64/libncbi-ngs.a.3.2.0 lib64/libncbi-ngs.a.%%PORTVERSION%%
lib64/libncbi-ngs.so lib64/libncbi-ngs.so
lib64/libncbi-ngs.so.3 lib64/libncbi-ngs.so.3
lib64/libncbi-ngs.so.3.2.0 lib64/libncbi-ngs.so.%%PORTVERSION%%
lib64/libngs-c++-static.a lib64/libngs-c++-static.a
lib64/libngs-c++.a lib64/libngs-c++.a
lib64/libngs-c++.a.3 lib64/libngs-c++.a.3
lib64/libngs-c++.a.3.2.0 lib64/libngs-c++.a.%%PORTVERSION%%
lib64/libngs-c++.so lib64/libngs-c++.so
lib64/libngs-c++.so.3 lib64/libngs-c++.so.3
lib64/libngs-c++.so.3.2.0 lib64/libngs-c++.so.%%PORTVERSION%%
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp