git: bb5aff4439a5 - main - biology/sra-tools: Update to 3.2.0
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Date: Wed, 29 Jan 2025 20:19:33 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=bb5aff4439a5d6cd28e45203961a7977804fc5c6
commit bb5aff4439a5d6cd28e45203961a7977804fc5c6
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-01-29 20:16:40 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-01-29 20:16:40 +0000
biology/sra-tools: Update to 3.2.0
Numerous fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/
Reported by: portscout
---
biology/sra-tools/Makefile | 8 +--
biology/sra-tools/distinfo | 10 +--
.../patch-ngs_ngs-java_examples_CMakeLists.txt | 11 +++
.../patch-ngs_ngs-python_examples_CMakeLists.txt | 11 +++
.../patch-ngs_ngs-sdk_examples_CMakeLists.txt | 20 ++++++
biology/sra-tools/pkg-plist | 80 +++++++++++-----------
6 files changed, 88 insertions(+), 52 deletions(-)
diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index 8ffd6b236fe5..a29cca6773cd 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -1,5 +1,5 @@
PORTNAME= sra-tools
-DISTVERSION= 3.1.1
+DISTVERSION= 3.2.0
CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org
@@ -53,12 +53,6 @@ pre-configure:
post-stage:
${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib64/*.${DISTVERSION}
- ${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools
- ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
- ${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR}
- ${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools
- ${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java
- ${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python
${MV} ${STAGEDIR}${JAVASHAREDIR}doc/ngs-doc/script-dir/jquery-[0-9]*.min.js \
${STAGEDIR}${JAVASHAREDIR}doc/ngs-doc/script-dir/jquery.min.js
diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo
index b69d1654ef45..d618e1c4cd92 100644
--- a/biology/sra-tools/distinfo
+++ b/biology/sra-tools/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1731806177
-SHA256 (ncbi-sra-tools-3.1.1_GH0.tar.gz) = 96b110bd5a30ad312e2f02552062b48a77d40c763e6aba5bb84e83662a505cf1
-SIZE (ncbi-sra-tools-3.1.1_GH0.tar.gz) = 45754110
-SHA256 (ncbi-ncbi-vdb-3.1.1_GH0.tar.gz) = e9766f259853c696be48e289b08cb5ae6e198d82d7ffee79f09ce7f720487991
-SIZE (ncbi-ncbi-vdb-3.1.1_GH0.tar.gz) = 19055901
+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
diff --git a/biology/sra-tools/files/patch-ngs_ngs-java_examples_CMakeLists.txt b/biology/sra-tools/files/patch-ngs_ngs-java_examples_CMakeLists.txt
new file mode 100644
index 000000000000..0c2a124d9ce3
--- /dev/null
+++ b/biology/sra-tools/files/patch-ngs_ngs-java_examples_CMakeLists.txt
@@ -0,0 +1,11 @@
+--- ngs/ngs-java/examples/CMakeLists.txt.orig 2024-11-18 12:32:32 UTC
++++ ngs/ngs-java/examples/CMakeLists.txt
+@@ -71,7 +71,7 @@ if ( Java_FOUND )
+
+ endif()
+
+- set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples-java )
++ set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools/java )
+
+ install(FILES ${SOURCES}
+ DESTINATION ${INSTALL_DEST}/examples )
diff --git a/biology/sra-tools/files/patch-ngs_ngs-python_examples_CMakeLists.txt b/biology/sra-tools/files/patch-ngs_ngs-python_examples_CMakeLists.txt
new file mode 100644
index 000000000000..901dbf055863
--- /dev/null
+++ b/biology/sra-tools/files/patch-ngs_ngs-python_examples_CMakeLists.txt
@@ -0,0 +1,11 @@
+--- ngs/ngs-python/examples/CMakeLists.txt.orig 2024-11-18 12:14:58 UTC
++++ ngs/ngs-python/examples/CMakeLists.txt
+@@ -54,7 +54,7 @@ if( Python3_EXECUTABLE )
+ RunAndDiff( RefTest "SRR1121656" )
+ endif()
+
+- set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples-python )
++ set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools/python )
+
+ install(FILES ${SOURCES} expected.txt
+ DESTINATION ${INSTALL_DEST} )
diff --git a/biology/sra-tools/files/patch-ngs_ngs-sdk_examples_CMakeLists.txt b/biology/sra-tools/files/patch-ngs_ngs-sdk_examples_CMakeLists.txt
new file mode 100644
index 000000000000..8287a7081fa0
--- /dev/null
+++ b/biology/sra-tools/files/patch-ngs_ngs-sdk_examples_CMakeLists.txt
@@ -0,0 +1,20 @@
+--- ngs/ngs-sdk/examples/CMakeLists.txt.orig 2024-11-18 12:15:33 UTC
++++ ngs/ngs-sdk/examples/CMakeLists.txt
+@@ -62,14 +62,14 @@ if ( SINGLE_CONFIG )
+ install(
+ FILES FragTest.cpp AlignTest.cpp AlignSliceTest.cpp PileupTest.cpp RefTest.cpp DumpReferenceFASTA.cpp
+ expected.txt
+- DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+ )
+ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Makefile.install
+- DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+ RENAME Makefile
+ )
+ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.install
+- DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+ RENAME README.txt
+ )
+ endif()
diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist
index f4ac6a2b7d44..1464c992d140 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.3.1.1
+bin/abi-dump.3.2.0
bin/align-info
bin/align-info.3
-bin/align-info.3.1.1
+bin/align-info.3.2.0
bin/cache-mgr
bin/cache-mgr.3
-bin/cache-mgr.3.1.1
+bin/cache-mgr.3.2.0
bin/check-corrupt
bin/check-corrupt.3
-bin/check-corrupt.3.1.1
+bin/check-corrupt.3.2.0
bin/fasterq-dump
-bin/fasterq-dump-orig.3.1.1
+bin/fasterq-dump-orig.3.2.0
bin/fasterq-dump.3
-bin/fasterq-dump.3.1.1
+bin/fasterq-dump.3.2.0
bin/fastq-dump
-bin/fastq-dump-orig.3.1.1
+bin/fastq-dump-orig.3.2.0
bin/fastq-dump.3
-bin/fastq-dump.3.1.1
+bin/fastq-dump.3.2.0
bin/illumina-dump
bin/illumina-dump.3
-bin/illumina-dump.3.1.1
+bin/illumina-dump.3.2.0
bin/kdbmeta
bin/kdbmeta.3
-bin/kdbmeta.3.1.1
+bin/kdbmeta.3.2.0
bin/ngs-pileup
bin/ngs-pileup.3
-bin/ngs-pileup.3.1.1
+bin/ngs-pileup.3.2.0
bin/prefetch
-bin/prefetch-orig.3.1.1
+bin/prefetch-orig.3.2.0
bin/prefetch.3
-bin/prefetch.3.1.1
+bin/prefetch.3.2.0
bin/rcexplain
bin/rcexplain.3
-bin/rcexplain.3.1.1
+bin/rcexplain.3.2.0
bin/ref-variation
bin/ref-variation.3
-bin/ref-variation.3.1.1
+bin/ref-variation.3.2.0
bin/sam-dump
-bin/sam-dump-orig.3.1.1
+bin/sam-dump-orig.3.2.0
bin/sam-dump.3
-bin/sam-dump.3.1.1
+bin/sam-dump.3.2.0
bin/sff-dump
bin/sff-dump.3
-bin/sff-dump.3.1.1
+bin/sff-dump.3.2.0
bin/sra-info
bin/sra-info.3
-bin/sra-info.3.1.1
+bin/sra-info.3.2.0
bin/sra-pileup
-bin/sra-pileup-orig.3.1.1
+bin/sra-pileup-orig.3.2.0
bin/sra-pileup.3
-bin/sra-pileup.3.1.1
+bin/sra-pileup.3.2.0
bin/sra-search
bin/sra-search.3
-bin/sra-search.3.1.1
+bin/sra-search.3.2.0
bin/sra-stat
bin/sra-stat.3
-bin/sra-stat.3.1.1
+bin/sra-stat.3.2.0
bin/srapath
-bin/srapath-orig.3.1.1
+bin/srapath-orig.3.2.0
bin/srapath.3
-bin/srapath.3.1.1
+bin/srapath.3.2.0
bin/sratools
bin/sratools.3
-bin/sratools.3.1.1
+bin/sratools.3.2.0
bin/test-sra
bin/test-sra.3
-bin/test-sra.3.1.1
+bin/test-sra.3.2.0
bin/var-expand
bin/var-expand.3
-bin/var-expand.3.1.1
+bin/var-expand.3.2.0
bin/vdb-config
bin/vdb-config.3
-bin/vdb-config.3.1.1
+bin/vdb-config.3.2.0
bin/vdb-decrypt
bin/vdb-decrypt.3
-bin/vdb-decrypt.3.1.1
+bin/vdb-decrypt.3.2.0
bin/vdb-dump
-bin/vdb-dump-orig.3.1.1
+bin/vdb-dump-orig.3.2.0
bin/vdb-dump.3
-bin/vdb-dump.3.1.1
+bin/vdb-dump.3.2.0
bin/vdb-encrypt
bin/vdb-encrypt.3
-bin/vdb-encrypt.3.1.1
+bin/vdb-encrypt.3.2.0
bin/vdb-validate
bin/vdb-validate.3
-bin/vdb-validate.3.1.1
+bin/vdb-validate.3.2.0
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.3.1.1
+lib64/libncbi-ngs-c++.a.3.2.0
lib64/libncbi-ngs-static.a
lib64/libncbi-ngs.a
lib64/libncbi-ngs.a.3
-lib64/libncbi-ngs.a.3.1.1
+lib64/libncbi-ngs.a.3.2.0
lib64/libncbi-ngs.so
lib64/libncbi-ngs.so.3
-lib64/libncbi-ngs.so.3.1.1
+lib64/libncbi-ngs.so.3.2.0
lib64/libngs-c++-static.a
lib64/libngs-c++.a
lib64/libngs-c++.a.3
-lib64/libngs-c++.a.3.1.1
+lib64/libngs-c++.a.3.2.0
lib64/libngs-c++.so
lib64/libngs-c++.so.3
-lib64/libngs-c++.so.3.1.1
+lib64/libngs-c++.so.3.2.0
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
@@ -271,9 +271,9 @@ lib64/libngs-c++.so.3.1.1
%%JAVASHAREDIR%%doc/ngs-doc/package-search-index.js
%%JAVASHAREDIR%%doc/ngs-doc/resources/glass.png
%%JAVASHAREDIR%%doc/ngs-doc/resources/x.png
-%%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery.min.js
%%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery-ui.min.css
%%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery-ui.min.js
+%%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery.min.js
%%JAVASHAREDIR%%doc/ngs-doc/script.js
%%JAVASHAREDIR%%doc/ngs-doc/search.js
%%JAVASHAREDIR%%doc/ngs-doc/serialized-form.html