From a57f4b8deadd7b3f93b7aac5b67b668f4686d949 Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Fri, 21 Mar 2025 06:27:22 -0500 Subject: [PATCH] biology/sra-tools: Update to 3.2.1 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 --- biology/sra-tools/Makefile | 4 +- biology/sra-tools/distinfo | 10 ++--- biology/sra-tools/pkg-plist | 78 ++++++++++++++++++------------------- 3 files changed, 47 insertions(+), 45 deletions(-) diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile index a29cca6773cd..3fa9ae25ebeb 100644 --- a/biology/sra-tools/Makefile +++ b/biology/sra-tools/Makefile @@ -1,5 +1,5 @@ PORTNAME= sra-tools -DISTVERSION= 3.2.0 +DISTVERSION= 3.2.1 CATEGORIES= biology java 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 +PLIST_SUB= PORTVERSION=${PORTVERSION} + pre-configure: # Reinplaces may follow static patches. Run "make clean patch" # before updating those patches so reinplaces do not get added to them. diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo index d618e1c4cd92..d74965cf7e1a 100644 --- a/biology/sra-tools/distinfo +++ b/biology/sra-tools/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1738157203 -SHA256 (ncbi-sra-tools-3.2.0_GH0.tar.gz) = 5ed9d0a61aa72c55566fb80b8b9293ad9006f528e7e11cba875d9377a0fc7b09 -SIZE (ncbi-sra-tools-3.2.0_GH0.tar.gz) = 60313243 -SHA256 (ncbi-ncbi-vdb-3.2.0_GH0.tar.gz) = 49fea92d9ec5ab38a5c06d1bcb057d1e7c9d4d39adcb7f31a3485ecc35bd5b77 -SIZE (ncbi-ncbi-vdb-3.2.0_GH0.tar.gz) = 19061110 +TIMESTAMP = 1742507022 +SHA256 (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 2558683c217ad2318833ab7731939617ed91dc79a6b1dee92bf88b56a1dc142a +SIZE (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 66684089 +SHA256 (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 535511984928ec5bac02a61fc6b4d1ca72a5b69c742f4882eabd32ed3a97621c +SIZE (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 19061776 diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist index 1464c992d140..e047e75fdafd 100644 --- a/biology/sra-tools/pkg-plist +++ b/biology/sra-tools/pkg-plist @@ -1,91 +1,91 @@ bin/abi-dump bin/abi-dump.3 -bin/abi-dump.3.2.0 +bin/abi-dump.%%PORTVERSION%% bin/align-info bin/align-info.3 -bin/align-info.3.2.0 +bin/align-info.%%PORTVERSION%% bin/cache-mgr bin/cache-mgr.3 -bin/cache-mgr.3.2.0 +bin/cache-mgr.%%PORTVERSION%% bin/check-corrupt bin/check-corrupt.3 -bin/check-corrupt.3.2.0 +bin/check-corrupt.%%PORTVERSION%% bin/fasterq-dump -bin/fasterq-dump-orig.3.2.0 +bin/fasterq-dump-orig.%%PORTVERSION%% bin/fasterq-dump.3 -bin/fasterq-dump.3.2.0 +bin/fasterq-dump.%%PORTVERSION%% bin/fastq-dump -bin/fastq-dump-orig.3.2.0 +bin/fastq-dump-orig.%%PORTVERSION%% bin/fastq-dump.3 -bin/fastq-dump.3.2.0 +bin/fastq-dump.%%PORTVERSION%% bin/illumina-dump bin/illumina-dump.3 -bin/illumina-dump.3.2.0 +bin/illumina-dump.%%PORTVERSION%% bin/kdbmeta bin/kdbmeta.3 -bin/kdbmeta.3.2.0 +bin/kdbmeta.%%PORTVERSION%% bin/ngs-pileup bin/ngs-pileup.3 -bin/ngs-pileup.3.2.0 +bin/ngs-pileup.%%PORTVERSION%% bin/prefetch -bin/prefetch-orig.3.2.0 +bin/prefetch-orig.%%PORTVERSION%% bin/prefetch.3 -bin/prefetch.3.2.0 +bin/prefetch.%%PORTVERSION%% bin/rcexplain bin/rcexplain.3 -bin/rcexplain.3.2.0 +bin/rcexplain.%%PORTVERSION%% bin/ref-variation bin/ref-variation.3 -bin/ref-variation.3.2.0 +bin/ref-variation.%%PORTVERSION%% bin/sam-dump -bin/sam-dump-orig.3.2.0 +bin/sam-dump-orig.%%PORTVERSION%% bin/sam-dump.3 -bin/sam-dump.3.2.0 +bin/sam-dump.%%PORTVERSION%% bin/sff-dump bin/sff-dump.3 -bin/sff-dump.3.2.0 +bin/sff-dump.%%PORTVERSION%% bin/sra-info bin/sra-info.3 -bin/sra-info.3.2.0 +bin/sra-info.%%PORTVERSION%% bin/sra-pileup -bin/sra-pileup-orig.3.2.0 +bin/sra-pileup-orig.%%PORTVERSION%% bin/sra-pileup.3 -bin/sra-pileup.3.2.0 +bin/sra-pileup.%%PORTVERSION%% bin/sra-search bin/sra-search.3 -bin/sra-search.3.2.0 +bin/sra-search.%%PORTVERSION%% bin/sra-stat bin/sra-stat.3 -bin/sra-stat.3.2.0 +bin/sra-stat.%%PORTVERSION%% bin/srapath -bin/srapath-orig.3.2.0 +bin/srapath-orig.%%PORTVERSION%% bin/srapath.3 -bin/srapath.3.2.0 +bin/srapath.%%PORTVERSION%% bin/sratools bin/sratools.3 -bin/sratools.3.2.0 +bin/sratools.%%PORTVERSION%% bin/test-sra bin/test-sra.3 -bin/test-sra.3.2.0 +bin/test-sra.%%PORTVERSION%% bin/var-expand bin/var-expand.3 -bin/var-expand.3.2.0 +bin/var-expand.%%PORTVERSION%% bin/vdb-config bin/vdb-config.3 -bin/vdb-config.3.2.0 +bin/vdb-config.%%PORTVERSION%% bin/vdb-decrypt bin/vdb-decrypt.3 -bin/vdb-decrypt.3.2.0 +bin/vdb-decrypt.%%PORTVERSION%% bin/vdb-dump -bin/vdb-dump-orig.3.2.0 +bin/vdb-dump-orig.%%PORTVERSION%% bin/vdb-dump.3 -bin/vdb-dump.3.2.0 +bin/vdb-dump.%%PORTVERSION%% bin/vdb-encrypt bin/vdb-encrypt.3 -bin/vdb-encrypt.3.2.0 +bin/vdb-encrypt.%%PORTVERSION%% bin/vdb-validate bin/vdb-validate.3 -bin/vdb-validate.3.2.0 +bin/vdb-validate.%%PORTVERSION%% include/ncbi-vdb/NGS.hpp include/ngs/Alignment.hpp include/ngs/AlignmentIterator.hpp @@ -184,21 +184,21 @@ jar/ngs-src.jar lib64/libncbi-ngs-c++-static.a lib64/libncbi-ngs-c++.a 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.a 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.3 -lib64/libncbi-ngs.so.3.2.0 +lib64/libncbi-ngs.so.%%PORTVERSION%% lib64/libngs-c++-static.a lib64/libngs-c++.a 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.3 -lib64/libngs-c++.so.3.2.0 +lib64/libngs-c++.so.%%PORTVERSION%% %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp