svn commit: r366842 - in head/biology/ugene: . files
Alexey Dokuchaev
danfe at FreeBSD.org
Mon Sep 1 07:39:00 UTC 2014
Author: danfe
Date: Mon Sep 1 07:38:59 2014
New Revision: 366842
URL: http://svnweb.freebsd.org/changeset/ports/366842
QAT: https://qat.redports.org/buildarchive/r366842/
Log:
- Update Unipro UGENE and documentation to version 1.14.0
- Remove patches integrated upstream (it's nice to have direct contact)
- Sort USES and pkg-plist, cleanup Makefile a bit while here
Approved by: maintainer (implicit)
Deleted:
head/biology/ugene/files/
Modified:
head/biology/ugene/Makefile
head/biology/ugene/distinfo
head/biology/ugene/pkg-plist
Modified: head/biology/ugene/Makefile
==============================================================================
--- head/biology/ugene/Makefile Mon Sep 1 07:31:53 2014 (r366841)
+++ head/biology/ugene/Makefile Mon Sep 1 07:38:59 2014 (r366842)
@@ -2,8 +2,8 @@
# $FreeBSD$
PORTNAME= ugene
-DISTVERSION= 1.13.1
-CATEGORIES= biology
+DISTVERSION= 1.14.0
+CATEGORIES= biology science
MASTER_SITES= http://ugene.unipro.ru/downloads/
DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
@@ -17,7 +17,7 @@ LICENSE= GPLv2
RUN_DEPENDS= bash:${PORTSDIR}/shells/bash
-USES= qmake execinfo
+USES= execinfo qmake
USE_GL= glu
USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \
qtestlib_build rcc_build uic_build imageformats_run \
@@ -26,8 +26,8 @@ USE_XORG= xtst
USE_LDCONFIG= yes
INSTALLS_ICONS= yes
-QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \
- INSTALL_MANDIR=${MAN1PREFIX}/man
+QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
+ INSTALL_MANDIR="${MAN1PREFIX}/man"
ALL_TARGET= release
DOCSDIR= ${DATADIR}/manuals
@@ -42,16 +42,19 @@ DOCS_DESC= Install official UGENE docume
CXXFLAGS+= -std=c++11
.endif
-.if ${ARCH} == "amd64"
+.if ${ARCH} == amd64
# XXX: need to manually tell the build we are on x64
QMAKE_ARGS+= CONFIG+=x64
-PLIST_SUB= NOX64="@comment "
+PLIST_SUB+= NOX64="@comment "
.else
-PLIST_SUB= NOX64=""
+PLIST_SUB+= NOX64=""
.endif
.if ${MACHINE_CPU:Msse2}
QMAKE_ARGS+= UGENE_SSE2_DETECTED=1
+PLIST_SUB+= SSE2=""
+.else
+PLIST_SUB+= SSE2="@comment "
.endif
post-extract:
@@ -62,40 +65,14 @@ post-patch:
@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
${WRKSRC}/src/gen_bin_script.cmd \
${WRKSRC}/installer/_common_data/ugene
- @${REINPLACE_CMD} -e '30s|^|#include <time.h>|' \
- ${WRKSRC}/src/plugins/dbi_bam/src/BAMDbiPlugin.h
- @${REINPLACE_CMD} -e 's|runTime=NULL|runTime=0|' \
- ${WRKSRC}/src/plugins/test_runner/src/TestViewReporter.h
- @${REINPLACE_CMD} -e 's|Q_OS_LINUX|Q_OS_UNIX|' \
- ${WRKSRC}/src/ugenem/src/main.cpp
- @(cd ${WRKSRC}/src/plugins/external_tool_support/src && \
- ${REINPLACE_CMD} -e 's/LINUX) || defined(Q_OS_MAC/UNIX/' \
- ExternalToolSupportPlugin.cpp \
- R/RSupport.cpp \
- blast/BlastAllSupport.cpp \
- blast/FormatDBSupport.cpp \
- blast_plus/BlastDBCmdSupport.cpp \
- blast_plus/BlastPlusSupport.cpp \
- bowtie/BowtieSupport.cpp \
- bowtie2/Bowtie2Support.cpp \
- bwa/BwaSupport.cpp \
- cap3/CAP3Support.cpp \
- clustalo/ClustalOSupport.cpp \
- clustalw/ClustalWSupport.cpp \
- cufflinks/CufflinksSupport.cpp \
- mrbayes/MrBayesSupport.cpp \
- perl/PerlSupport.cpp \
- python/PythonSupport.cpp \
- samtools/BcfToolsSupport.cpp \
- samtools/SamToolsExtToolSupport.cpp \
- spidey/SpideySupport.cpp \
- tcoffee/TCoffeeSupport.cpp \
- tophat/TopHatSupport.cpp \
- utils/ExternalToolSearchTask.cpp)
-
-post-configure:
- @${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \
- ${WRKSRC}/src/ugenecl/Makefile.Release \
- ${WRKSRC}/src/ugeneui/Makefile.Release
+ @${REINPLACE_CMD} -e '/readproc\.h/d' \
+ ${WRKSRC}/src/corelibs/U2Core/src/globals/AppResources.cpp
+ @${REINPLACE_CMD} -e '1000d' \
+ ${WRKSRC}/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/string.h
+ @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}|' \
+ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
+.for x in ugenecl ugeneui plugins_checker
+ @${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro
+.endfor
.include <bsd.port.post.mk>
Modified: head/biology/ugene/distinfo
==============================================================================
--- head/biology/ugene/distinfo Mon Sep 1 07:31:53 2014 (r366841)
+++ head/biology/ugene/distinfo Mon Sep 1 07:38:59 2014 (r366842)
@@ -1,8 +1,8 @@
-SHA256 (ugene/ugene-1.13.1.tar.gz) = 00814743de631cc144e6f01955a5183bc668684de073f600e6491b504a7760c1
-SIZE (ugene/ugene-1.13.1.tar.gz) = 19098188
-SHA256 (ugene/QueryDesigner_UserManual.pdf) = 3c5bd735c02b7ac24bd319823fde2d175b750adc1c37fe7b17e2009452a00ddd
-SIZE (ugene/QueryDesigner_UserManual.pdf) = 1306825
-SHA256 (ugene/UniproUGENE_UserManual.pdf) = 6c682c86f47a4c337eb4acdf0ae23ffa1b7fef1337d11e631655bfc943167b46
-SIZE (ugene/UniproUGENE_UserManual.pdf) = 12166178
-SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = dd9a5e5860867a9a8f22d946dd94c34ee406aa648ff3d4220b0c2c5486e4bbeb
-SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 8963233
+SHA256 (ugene/ugene-1.14.0.tar.gz) = e54f67d54378fcb375029267bc1ae75aec5e6e4e7c9977184be5865475ef2c42
+SIZE (ugene/ugene-1.14.0.tar.gz) = 19777919
+SHA256 (ugene/QueryDesigner_UserManual.pdf) = 2add11809ecc3225abfef417ad8d5435fed76a662081f461abb36e3d4b31cfcd
+SIZE (ugene/QueryDesigner_UserManual.pdf) = 824781
+SHA256 (ugene/UniproUGENE_UserManual.pdf) = c4aa20246988978c6b40a06f7753f78d204ee3155cb8876a3d665b9ebf5641db
+SIZE (ugene/UniproUGENE_UserManual.pdf) = 12263913
+SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 9dc5b25bdc8d7af1473f5a860debebfd238bfef018cc7a9d69816354efcfa202
+SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 8639016
Modified: head/biology/ugene/pkg-plist
==============================================================================
--- head/biology/ugene/pkg-plist Mon Sep 1 07:31:53 2014 (r366841)
+++ head/biology/ugene/pkg-plist Mon Sep 1 07:38:59 2014 (r366842)
@@ -51,36 +51,20 @@ lib/ugene/libugenedb.so
lib/ugene/libugenedb.so.1
lib/ugene/libugenedb.so.1.0
lib/ugene/libugenedb.so.1.0.0
-lib/ugene/plugins/libbrowser_support.so
-lib/ugene/plugins/libbrowser_support.so.1
-lib/ugene/plugins/libbrowser_support.so.1.0
-lib/ugene/plugins/libbrowser_support.so.1.0.0
-lib/ugene/plugins/liblinkdata_support.so
-lib/ugene/plugins/liblinkdata_support.so.1
-lib/ugene/plugins/liblinkdata_support.so.1.0
-lib/ugene/plugins/liblinkdata_support.so.1.0.0
-lib/ugene/plugins/libvariants.so
-lib/ugene/plugins/libvariants.so.1
-lib/ugene/plugins/libvariants.so.1.0
-lib/ugene/plugins/libvariants.so.1.0.0
-lib/ugene/plugins/linkdata_support.license
-lib/ugene/plugins/linkdata_support.plugin
-lib/ugene/plugins/variants.license
-lib/ugene/plugins/variants.plugin
lib/ugene/plugins/CoreTests.license
lib/ugene/plugins/CoreTests.plugin
lib/ugene/plugins/GUITestBase.license
lib/ugene/plugins/GUITestBase.plugin
lib/ugene/plugins/annotator.license
lib/ugene/plugins/annotator.plugin
-lib/ugene/plugins/browser_support.license
-lib/ugene/plugins/browser_support.plugin
lib/ugene/plugins/api_tests.license
lib/ugene/plugins/api_tests.plugin
lib/ugene/plugins/ball.license
lib/ugene/plugins/ball.plugin
lib/ugene/plugins/biostruct3d_view.license
lib/ugene/plugins/biostruct3d_view.plugin
+lib/ugene/plugins/browser_support.license
+lib/ugene/plugins/browser_support.plugin
lib/ugene/plugins/chroma_view.license
lib/ugene/plugins/chroma_view.plugin
lib/ugene/plugins/circular_view.license
@@ -109,6 +93,8 @@ lib/ugene/plugins/gor4.license
lib/ugene/plugins/gor4.plugin
lib/ugene/plugins/hmm2.license
lib/ugene/plugins/hmm2.plugin
+%%SSE2%%lib/ugene/plugins/hmm3.license
+%%SSE2%%lib/ugene/plugins/hmm3.plugin
lib/ugene/plugins/kalign.license
lib/ugene/plugins/kalign.plugin
lib/ugene/plugins/libCoreTests.so
@@ -135,6 +121,10 @@ lib/ugene/plugins/libbiostruct3d_view.so
lib/ugene/plugins/libbiostruct3d_view.so.1
lib/ugene/plugins/libbiostruct3d_view.so.1.0
lib/ugene/plugins/libbiostruct3d_view.so.1.0.0
+lib/ugene/plugins/libbrowser_support.so
+lib/ugene/plugins/libbrowser_support.so.1
+lib/ugene/plugins/libbrowser_support.so.1.0
+lib/ugene/plugins/libbrowser_support.so.1.0.0
lib/ugene/plugins/libchroma_view.so
lib/ugene/plugins/libchroma_view.so.1
lib/ugene/plugins/libchroma_view.so.1.0
@@ -191,10 +181,18 @@ lib/ugene/plugins/libhmm2.so
lib/ugene/plugins/libhmm2.so.1
lib/ugene/plugins/libhmm2.so.1.0
lib/ugene/plugins/libhmm2.so.1.0.0
+%%SSE2%%lib/ugene/plugins/libhmm3.so
+%%SSE2%%lib/ugene/plugins/libhmm3.so.1
+%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0
+%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0.0
lib/ugene/plugins/libkalign.so
lib/ugene/plugins/libkalign.so.1
lib/ugene/plugins/libkalign.so.1.0
lib/ugene/plugins/libkalign.so.1.0.0
+lib/ugene/plugins/liblinkdata_support.so
+lib/ugene/plugins/liblinkdata_support.so.1
+lib/ugene/plugins/liblinkdata_support.so.1.0
+lib/ugene/plugins/liblinkdata_support.so.1.0.0
lib/ugene/plugins/libopencl_support.so
lib/ugene/plugins/libopencl_support.so.1
lib/ugene/plugins/libopencl_support.so.1.0
@@ -259,6 +257,10 @@ lib/ugene/plugins/libtest_runner.so.1.0.
%%NOX64%%lib/ugene/plugins/libumuscle.so.1
%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0
%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0.0
+lib/ugene/plugins/libvariants.so
+lib/ugene/plugins/libvariants.so.1
+lib/ugene/plugins/libvariants.so.1.0
+lib/ugene/plugins/libvariants.so.1.0.0
lib/ugene/plugins/libweight_matrix.so
lib/ugene/plugins/libweight_matrix.so.1
lib/ugene/plugins/libweight_matrix.so.1.0
@@ -267,6 +269,8 @@ lib/ugene/plugins/libworkflow_designer.s
lib/ugene/plugins/libworkflow_designer.so.1
lib/ugene/plugins/libworkflow_designer.so.1.0
lib/ugene/plugins/libworkflow_designer.so.1.0.0
+lib/ugene/plugins/linkdata_support.license
+lib/ugene/plugins/linkdata_support.plugin
lib/ugene/plugins/opencl_support.license
lib/ugene/plugins/opencl_support.plugin
lib/ugene/plugins/orf_marker.license
@@ -299,10 +303,13 @@ lib/ugene/plugins/test_runner.license
lib/ugene/plugins/test_runner.plugin
%%NOX64%%lib/ugene/plugins/umuscle.license
%%NOX64%%lib/ugene/plugins/umuscle.plugin
+lib/ugene/plugins/variants.license
+lib/ugene/plugins/variants.plugin
lib/ugene/plugins/weight_matrix.license
lib/ugene/plugins/weight_matrix.plugin
lib/ugene/plugins/workflow_designer.license
lib/ugene/plugins/workflow_designer.plugin
+lib/ugene/plugins_checker
lib/ugene/transl_cs.qm
lib/ugene/transl_en.qm
lib/ugene/transl_ru.qm
@@ -366,6 +373,7 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/cmdline/convert-seq.uwl
%%DATADIR%%/cmdline/das_annotation.uwl
%%DATADIR%%/cmdline/extract-sequence.uwl
+%%DATADIR%%/cmdline/extract_consensus.uwl
%%DATADIR%%/cmdline/fetch-sequence.uwl
%%DATADIR%%/cmdline/find-orfs.uwl
%%DATADIR%%/cmdline/find-repeats.uwl
@@ -387,7 +395,16 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/cmdline/sitecon-build.uwl
%%DATADIR%%/cmdline/sitecon-search.uwl
%%DATADIR%%/cmdline/snp.uwl
+%%DATADIR%%/custom_annotations/plasmid_features.txt
%%DATADIR%%/enzymes/2013_08_01.bairoch.gz
+%%DATADIR%%/genome_lengths/danRer7.genome
+%%DATADIR%%/genome_lengths/ecoli.genome
+%%DATADIR%%/genome_lengths/hg18.genome
+%%DATADIR%%/genome_lengths/hg19.genome
+%%DATADIR%%/genome_lengths/mm10.genome
+%%DATADIR%%/genome_lengths/mm8.genome
+%%DATADIR%%/genome_lengths/mm9.genome
+%%DATADIR%%/genome_lengths/test.genome
%%DATADIR%%/license
%%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf
%%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf
@@ -1141,8 +1158,8 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/query_samples/RepeatsWithORF.uql
%%DATADIR%%/query_samples/SimpleGene.uql
%%DATADIR%%/samples/ABIF/A01.abi
-%%DATADIR%%/samples/ACE/K26.ace
%%DATADIR%%/samples/ACE/BL060C3.ace
+%%DATADIR%%/samples/ACE/K26.ace
%%DATADIR%%/samples/Assembly/chrM.fa
%%DATADIR%%/samples/Assembly/chrM.sam
%%DATADIR%%/samples/Assembly/chrM.sorted.bam
@@ -1372,6 +1389,8 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl
%%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl
%%DATADIR%%/workflow_samples/Conversions/seq2gen.uwl
+%%DATADIR%%/workflow_samples/Custom elements/casava-fastq-filter.uwl
+%%DATADIR%%/workflow_samples/Custom elements/fastq-trimmer.uwl
%%DATADIR%%/workflow_samples/Custom elements/script-dump-sequence-info.uwl
%%DATADIR%%/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
%%DATADIR%%/workflow_samples/Custom elements/script-quality-filter.uwl
@@ -1395,12 +1414,15 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
+%%DATADIR%%/workflow_samples/Scenarios/extract_consensus.uwl
%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
%%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl
%%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
%%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
%%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl
+%%DATADIR%%/workflow_samples/users/CASAVA FASTQ filter.usa
%%DATADIR%%/workflow_samples/users/Dump sequence info.usa
+%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa
%%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
%%DATADIR%%/workflow_samples/users/QualityFilter.usa
@dirrm %%DATADIR%%/workflow_samples/users
@@ -1456,7 +1478,9 @@ share/pixmaps/ugene.xpm
@dirrm %%DATADIR%%/position_weight_matrix/JASPAR
@dirrm %%DATADIR%%/position_weight_matrix
%%PORTDOCS%%@dirrm %%DOCSDIR%%
+ at dirrm %%DATADIR%%/genome_lengths
@dirrm %%DATADIR%%/enzymes
+ at dirrm %%DATADIR%%/custom_annotations
@dirrm %%DATADIR%%/cmdline
@dirrm %%DATADIR%%/biostruct3d_plugin
@dirrm %%DATADIR%%/back_translation/Yeast
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