diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index 00c5fcf8e33a..c7e44cc879ed 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -1,74 +1,75 @@ # Created by: J. Bacon PORTNAME= ucsc-userapps -DISTVERSION= 413 +DISTVERSION= 414 CATEGORIES= biology perl5 python MASTER_SITES= http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ DISTNAME= userApps.v${PORTVERSION}.src MAINTAINER= jwb@FreeBSD.org COMMENT= Command line tools from the UCSC Genome Browser project LICENSE= UCSC-GB LICENSE_NAME= UCSC Genome Browser License -LICENSE_TEXT= To the best of our knowledge, all of the tools installed by\ - this port are freely available. However, a license is\ - required for commercial download and installation of some\ - binaries and source code in the UCSC Genome Browser\ - distribution.\n\nContact UCSC directly if you are using these\ - tools for commercial purposes.\n\nSee\ +LICENSE_TEXT= Some tools installed by this port require a license for\ + commercial use.\n\nContact UCSC directly if you are using\ + these tools for commercial purposes.\n\nSee\ https://genome.ucsc.edu/license/ for full terms. LICENSE_PERMS= no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell ONLY_FOR_ARCHS= amd64 ONLY_FOR_ARCHS_REASON= _mm_popcnt_u64 BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libiconv.so:converters/libiconv \ libmysqlclient.so:databases/mysql57-client \ libpng.so:graphics/png RUN_DEPENDS= bash:shells/bash USES= gmake localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz +RESTRICTED= Redistribution is limited, see license + SHEBANG_FILES= kent/src/checkUmask.sh \ kent/src/utils/bigHeat \ kent/src/utils/chromToUcsc/chromToUcsc \ kent/src/utils/tdbRename \ kent/src/utils/tdbSort \ kent/src/utils/trackDbIndexBb/trackDbIndexBb \ kent/src/utils/ucscApiClient \ kent/src/utils/webSync WRKSRC= ${WRKDIR}/userApps CFLAGS+= -fcommon MAKEFILE= [Mm]akefile MAKE_ENV= BINDIR=${WRKSRC}/bin SUB_FILES= ucsc-shell -# Build only non-commercial tools +# Build mostly non-commercial tools. There is some leakage of proprietary +# code from the libraries per conversation with UCSC. Work to resolve this +# is ongoing. do-build: @${MV} ${WRKSRC}/kent/src/inc/uuid.h ${WRKSRC}/kent/src/inc/my_uuid.h @${MKDIR} ${WRKSRC}/bin @(cd ${WRKSRC}/kent/src/lib && ${DO_MAKE_BUILD}) @(cd ${WRKSRC}/kent/src/htslib && ${DO_MAKE_BUILD}) @(cd ${WRKSRC}/kent/src/jkOwnLib && ${DO_MAKE_BUILD}) @(cd ${WRKSRC}/kent/src/hg/lib && ${DO_MAKE_BUILD}) @(cd ${WRKSRC}/kent/src/utils && ${DO_MAKE_BUILD}) do-install: @${MKDIR} ${WRKSRC}/scripts ${WRKSRC}/binaries @${CP} $$(file ${WRKSRC}/bin/* | fgrep ELF | cut -d : -f 1) \ ${WRKSRC}/binaries @${CP} $$(file ${WRKSRC}/bin/* | fgrep -v ELF | cut -d : -f 1) \ ${WRKSRC}/scripts @${MKDIR} ${STAGEDIR}${PREFIX}/userapps/bin ${INSTALL_PROGRAM} ${WRKSRC}/binaries/* \ ${STAGEDIR}${PREFIX}/userapps/bin ${INSTALL_SCRIPT} ${WRKSRC}/scripts/* \ ${STAGEDIR}${PREFIX}/userapps/bin ${INSTALL_SCRIPT} ${WRKDIR}/ucsc-shell \ ${STAGEDIR}${PREFIX}/bin .include diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo index a75f1d9a21b0..cc2c9ed9a4e7 100644 --- a/biology/ucsc-userapps/distinfo +++ b/biology/ucsc-userapps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1619366655 -SHA256 (userApps.v413.src.tgz) = 91c51fec26bc61ea0dd9c4d0d13c76ce26e1c7d7f7dddbd3067c70beaec0af19 -SIZE (userApps.v413.src.tgz) = 19186621 +TIMESTAMP = 1621027743 +SHA256 (userApps.v414.src.tgz) = 36910b5c84ea613d4eb6ccb9572f3b34d929c5571578b1d91013391895638ab0 +SIZE (userApps.v414.src.tgz) = 19195157 diff --git a/biology/ucsc-userapps/pkg-plist b/biology/ucsc-userapps/pkg-plist index 3766142e1e8b..e8304be64af2 100644 --- a/biology/ucsc-userapps/pkg-plist +++ b/biology/ucsc-userapps/pkg-plist @@ -1,135 +1,136 @@ bin/ucsc-shell userapps/bin/aNotB userapps/bin/addCols userapps/bin/ave userapps/bin/aveCols userapps/bin/bamToPsl userapps/bin/bedClip userapps/bin/bedCommonRegions userapps/bin/bedGeneParts userapps/bin/bedGraphPack userapps/bin/bedGraphToBigWig userapps/bin/bedJoinTabOffset userapps/bin/bedPileUps userapps/bin/bedRemoveOverlap userapps/bin/bedRestrictToPositions userapps/bin/bedToBigBed userapps/bin/bigBedInfo userapps/bin/bigBedNamedItems userapps/bin/bigBedSummary userapps/bin/bigBedToBed userapps/bin/bigWigAverageOverBed userapps/bin/bigWigCat userapps/bin/bigWigCluster userapps/bin/bigWigCorrelate userapps/bin/bigWigInfo userapps/bin/bigWigMerge userapps/bin/bigWigSummary userapps/bin/bigWigToBedGraph userapps/bin/bigWigToWig userapps/bin/calc userapps/bin/catDir userapps/bin/catUncomment userapps/bin/ccCp userapps/bin/chopFaLines userapps/bin/clusterMatrixToBarChartBed userapps/bin/colTransform userapps/bin/convolve userapps/bin/countChars userapps/bin/cpg_lh userapps/bin/detab userapps/bin/dnsInfo userapps/bin/endsInLf userapps/bin/faAlign userapps/bin/faCmp userapps/bin/faCount userapps/bin/faFilter userapps/bin/faFilterN userapps/bin/faFlyBaseToUcsc userapps/bin/faFrag userapps/bin/faGapLocs userapps/bin/faGapSizes userapps/bin/faNcbiToUcsc userapps/bin/faNoise userapps/bin/faOneRecord userapps/bin/faPolyASizes userapps/bin/faRandomize userapps/bin/faRc +userapps/bin/faRenameRecords userapps/bin/faSimplify userapps/bin/faSize userapps/bin/faSomeRecords userapps/bin/faSplit userapps/bin/faToFastq userapps/bin/faToNib userapps/bin/faToTab userapps/bin/faToTwoBit userapps/bin/faTrans userapps/bin/faTrimPolyA userapps/bin/faTrimRead userapps/bin/fastqStatsAndSubsample userapps/bin/fastqToFa userapps/bin/findMotif userapps/bin/fixCr userapps/bin/gapSplit userapps/bin/gffPeek userapps/bin/git-reports userapps/bin/gmtime userapps/bin/headRest userapps/bin/htmlCheck userapps/bin/htmlPics userapps/bin/jkUniq userapps/bin/lineCount userapps/bin/linesToRa userapps/bin/localtime userapps/bin/mktime userapps/bin/newProg userapps/bin/newPythonProg userapps/bin/nibFrag userapps/bin/nibSize userapps/bin/nt4Frag userapps/bin/paraFetch userapps/bin/paraSync userapps/bin/pslLiftSubrangeBlat userapps/bin/pslPosTarget userapps/bin/pslRemoveFrameShifts userapps/bin/pslScore userapps/bin/pslToPslx userapps/bin/pslToXa userapps/bin/raSqlQuery userapps/bin/raToLines userapps/bin/raToTab userapps/bin/randomLines userapps/bin/rmFaDups userapps/bin/rowsToCols userapps/bin/scaffoldFaToAgp userapps/bin/scrambleFa userapps/bin/sizeof userapps/bin/spacedToTab userapps/bin/splitFile userapps/bin/splitFileByColumn userapps/bin/strexCalc userapps/bin/stringify userapps/bin/subChar userapps/bin/subColumn userapps/bin/subs userapps/bin/tableSum userapps/bin/tailLines userapps/bin/textHist2 userapps/bin/textHistogram userapps/bin/tickToDate userapps/bin/toLower userapps/bin/toUpper userapps/bin/trackDbIndexBb userapps/bin/twoBitDup userapps/bin/twoBitInfo userapps/bin/twoBitToFa userapps/bin/udcCleanup userapps/bin/undupFa userapps/bin/upper userapps/bin/vcfFilter userapps/bin/venn userapps/bin/verticalSplitSqlTable userapps/bin/weedLines userapps/bin/wigCorrelate userapps/bin/wigToBigWig userapps/bin/wordLine