git: a57f4b8deadd - main - biology/sra-tools: Update to 3.2.1
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Date: Fri, 21 Mar 2025 11:29:40 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=a57f4b8deadd7b3f93b7aac5b67b668f4686d949
commit a57f4b8deadd7b3f93b7aac5b67b668f4686d949
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-03-21 11:27:22 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-03-21 11:27:22 +0000
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