From nobody Wed Jan 29 20:19:33 2025 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4YjtmP4RsSz5lwMW; Wed, 29 Jan 2025 20:19:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YjtmP3mhLz3cwB; Wed, 29 Jan 2025 20:19:33 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1738181973; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=Ztm+m5kloOx2jJvmsr85NrLUkr/U22xXCM8eVPyC8b4=; b=lvEh93kol8X9E2gvhPk2nwes6aGYn1zU4Mz9MtWZpR5Na704dVfRQDGJgWnxyVWjYtyAJW CgTo9Ir1aqYlPh5XgfvONHWd4cdecgRqlMw5V8Y11xMwQxruk5BLcy+5zPtzvniGr/w/z1 wfmDmEAPGxXganG/b5+HXiUXZP/p8tHj6A6hERGj3G/s4vgWcosxdoCrZUGUCZFN8Ljneg G2BnomTS14bs6Po1Tp3SASHFOQ8XYVxeDCT7pObSjYCmQVfRZQ5oT2+L7pS8dXvkdaCzQ+ dMAwV3tqrvhfCJxkGMumiG6BEoUHZvQVAwRQbt7Q5A1ad2ikCAI1za+2afsdLg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1738181973; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=Ztm+m5kloOx2jJvmsr85NrLUkr/U22xXCM8eVPyC8b4=; b=Ehcg9xdbFtFpgNbNhPH0ScfCEXoj46b+gYDDtQMAe6VWP75dy9x7Fo/7T4n+idP45PY6sA 3WPOnrhebsIpQ5YXsnxPnmpCf4QNnkR6k6CWrnqIFSNgdH0e3QqKNmzabpuq7rrJlhnF49 2qx8PxwpepGi7RwGxBzT1CQkdtd/rLUrrSHDswZ3Pe0kCW9f2HTVY4zjnyr5t0exeb+eUa vj4NFZkiWJlVbVB/sWHaJGLDw5TuJI/6FeTCsbxwJ/WuIjtG1zYmtqf4VlSQJ85sAtGcmJ kjXy5iOZDRwsFRFVLIasJrk/kM59sqkAmyYc4yVgeDVq7gYpkFZxMvlDX83cEg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1738181973; a=rsa-sha256; cv=none; b=TGop/cmdLeMoskBXYgHRX/HJjpJyTOMWFN9g+LwP+c8Ciw8MVdenHz8DLaYjzgdXzeLWEE 7U3FaERftOKxjPB2oDt9afIc39MpovELW6FKZ8Fb9NOqrCOFVeQPEYlmNZcBLQiuvPayPT CPn4VshCe20scqFd88mPbhK9mG35eEtdwDfMPP+xzwI+dIuHp96VVdEmjRtsaAHWe7TImK PPARGNohTXRMbfyCLKyXf8neoubllpwXf2kuuLGN8a4SFRG4uq42EvV1SJJrx6FSdDet+7 fjf/1UDFKPUvpBVzhgJq5z2w/SCAuhxMWVT/s08M7tVliAtai0umuCJZ5OZA/g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4YjtmP3CPVzrf; Wed, 29 Jan 2025 20:19:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 50TKJXff016492; Wed, 29 Jan 2025 20:19:33 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50TKJX6X016489; Wed, 29 Jan 2025 20:19:33 GMT (envelope-from git) Date: Wed, 29 Jan 2025 20:19:33 GMT Message-Id: <202501292019.50TKJX6X016489@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: bb5aff4439a5 - main - biology/sra-tools: Update to 3.2.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: bb5aff4439a5d6cd28e45203961a7977804fc5c6 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=bb5aff4439a5d6cd28e45203961a7977804fc5c6 commit bb5aff4439a5d6cd28e45203961a7977804fc5c6 Author: Jason W. Bacon AuthorDate: 2025-01-29 20:16:40 +0000 Commit: Jason W. Bacon 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