sync/ports
1
0
Fork 0
mirror of https://git.freebsd.org/ports.git synced 2025-04-28 09:36:41 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions

biology/sra-tools: Update to 3.2.0

Browse source 
Numerous fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2025-01-29 14:16:40 -06:00
parent cfbada1909
commit bb5aff4439
6 changed files with 88 additions and 52 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

8
biology/sra-tools/Makefile
View file

@ -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

10
biology/sra-tools/distinfo
View file

@ -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

11
biology/sra-tools/files/patch-ngs_ngs-java_examples_CMakeLists.txt Normal file
View file

@ -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 )

11
biology/sra-tools/files/patch-ngs_ngs-python_examples_CMakeLists.txt Normal file
View file

@ -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} )

20
biology/sra-tools/files/patch-ngs_ngs-sdk_examples_CMakeLists.txt Normal file
View file

@ -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()

80
biology/sra-tools/pkg-plist
View file

@ -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