diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index 326c385a62c9..bf4f9d8f4cb6 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -1,71 +1,72 @@ PORTNAME= ucsc-userapps -DISTVERSION= 474 +DISTVERSION= 502 CATEGORIES= biology perl5 python MASTER_SITES= https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ DISTNAME= userApps.v${DISTVERSION}.src MAINTAINER= jwb@FreeBSD.org COMMENT= Command line tools from the UCSC Genome Browser project WWW= https://hgdownload.cse.ucsc.edu/admin/exe/ # Note: Some tools in the source dist are non-free for commercial use. # If they are added to the install, the license below must be changed # and packaging forbidden. LICENSE= MIT BUILD_DEPENDS= bash:shells/bash -# FIXME: Switch from mysql to mariadb -LIB_DEPENDS= libmysqlclient.so:databases/mysql80-client \ +LIB_DEPENDS= libfreetype.so:print/freetype2 \ libunwind.so:devel/libunwind \ - libfreetype.so:print/freetype2 \ - libpng.so:graphics/png + libcurl.so:ftp/curl \ + libpng16.so:graphics/png RUN_DEPENDS= bash:shells/bash -USES= gmake iconv localbase:ldflags shebangfix perl5 python ssl tar:tgz +USES= gmake iconv localbase:ldflags mysql:client shebangfix perl5 python ssl tar:tgz 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 \ - kent/src/utils/bigGuessDb/bigGuessDb + kent/src/utils/bigGuessDb/bigGuessDb \ + kent/src/utils/expMatrixToBarchartBed \ + kent/src/utils/hubtools WRKSRC= ${WRKDIR}/userApps CFLAGS+= -fcommon MAKEFILE= [Mm]akefile MAKE_ENV= BINDIR=${WRKSRC}/bin SUB_FILES= ucsc-shell # 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: @(test -f ${WRKSRC}/kent/src/inc/my_uuid.h || ${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/submodules/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}) ${CC} -DUCSC_PREFIX="\"${PREFIX}/userapps\"" ${FILESDIR}/kent.c -o ${WRKDIR}/kent do-install: @${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 ${INSTALL_PROGRAM} ${WRKDIR}/kent ${STAGEDIR}${LOCALBASE}/bin .include diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo index ea61209e348b..919c8cd4f118 100644 --- a/biology/ucsc-userapps/distinfo +++ b/biology/ucsc-userapps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1732796640 -SHA256 (userApps.v474.src.tgz) = 87c465169b1246c3d2f56ea415461b7b2a4fb24bf5b7b95a3b590274cc7daec7 -SIZE (userApps.v474.src.tgz) = 24402279 +TIMESTAMP = 1788211114 +SHA256 (userApps.v502.src.tgz) = 38e29dbf7c1e6d49aaf358014960c5781fd59aa3b7b406dadc9557c98e895f22 +SIZE (userApps.v502.src.tgz) = 29944124 diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c deleted file mode 100644 index 9f2b33c711da..000000000000 --- a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c +++ /dev/null @@ -1,11 +0,0 @@ ---- kent/src/hg/encode3/eap/eapFinish/eapFinish.c.orig 2024-10-16 04:15:27 UTC -+++ kent/src/hg/encode3/eap/eapFinish/eapFinish.c -@@ -3,7 +3,7 @@ - - /* Copyright (C) 2014 The Regents of the University of California - * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ --#include -+#include - #include "common.h" - #include "linefile.h" - #include "hash.h" diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_inc_hui.h b/biology/ucsc-userapps/files/patch-kent_src_hg_inc_hui.h new file mode 100644 index 000000000000..d8bc03c19158 --- /dev/null +++ b/biology/ucsc-userapps/files/patch-kent_src_hg_inc_hui.h @@ -0,0 +1,11 @@ +--- kent/src/hg/inc/hui.h.orig 2026-08-31 20:04:01 UTC ++++ kent/src/hg/inc/hui.h +@@ -1607,7 +1607,7 @@ int defaultFieldLocation(char *field); + /* Sometimes we get bigBed filters with field names that are not in the AS file. + * Try to guess what the user means. */ + +-void printInfoIconSvg(); ++void printInfoIconSvg(char *color); + /* Print just info icon (i) as svg to stdout */ + + void printInfoIconColor(char *mouseover, char *color); diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c new file mode 100644 index 000000000000..55a8b2da3d01 --- /dev/null +++ b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c @@ -0,0 +1,12 @@ +--- kent/src/hg/lib/jksql.c.orig 2026-08-31 20:06:42 UTC ++++ kent/src/hg/lib/jksql.c +@@ -1140,7 +1140,8 @@ else // TURN VERIFICATION OFF + else // TURN VERIFICATION OFF + { + #if !defined(MARIADB_BASE_VERSION) && defined(MYSQL_VERSION_ID) && (MYSQL_VERSION_ID >= 80000) // OVER-RIDE DEFAULT COMPILED IN. +- mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_PREFERRED); ++ int mode_arg = SSL_MODE_PREFERRED; ++ mysql_options(conn, MYSQL_OPT_SSL_MODE, &mode_arg); + #else + my_bool flag = FALSE; + mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag); diff --git a/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk b/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk index c04678ded9e1..aa080aa18bf9 100644 --- a/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk +++ b/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk @@ -1,12 +1,12 @@ ---- kent/src/inc/common.mk.orig 2024-10-16 04:15:27 UTC +--- kent/src/inc/common.mk.orig 2026-07-07 22:13:59 UTC +++ kent/src/inc/common.mk -@@ -65,6 +65,9 @@ ifeq ($(UNAME_S),Darwin) +@@ -124,6 +124,9 @@ ifeq ($(UNAME_S),Darwin) ifneq ($(wildcard /opt/local/lib/libiconv.a),) ICONVLIB = /opt/local/lib/libiconv.a endif + ifeq ($(UNAME_S),FreeBSD) + ICONVLIB=-L${LOCALBASE}/lib -liconv + endif - ifneq ($(wildcard /opt/homebrew/lib/libmysqlclient.a),) - MYSQLLIBS = /opt/homebrew/lib/libmysqlclient.a - endif + ifneq ($(wildcard /usr/local/Cellar/mariadb/11.6.2/lib/libmariadbclient.a),) + MYSQLLIBS = /usr/local/Cellar/mariadb/11.6.2/lib/libmariadbclient.a + else diff --git a/biology/ucsc-userapps/files/patch-kent_src_submodules_htslib_Makefile b/biology/ucsc-userapps/files/patch-kent_src_submodules_htslib_Makefile new file mode 100644 index 000000000000..6d4e90f73e14 --- /dev/null +++ b/biology/ucsc-userapps/files/patch-kent_src_submodules_htslib_Makefile @@ -0,0 +1,33 @@ +--- kent/src/submodules/htslib/Makefile.orig 2026-08-30 18:17:35 UTC ++++ kent/src/submodules/htslib/Makefile +@@ -22,9 +22,9 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib ++CC ?= gcc ++AR ?= ar ++RANLIB ?= ranlib + + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl +@@ -35,14 +35,14 @@ CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 +-CFLAGS = -g -Wall -O2 -fvisibility=hidden ++CFLAGS ?= -g -Wall -O2 -fvisibility=hidden + EXTRA_CFLAGS_PIC = -fpic + TARGET_CFLAGS = +-LDFLAGS = -fvisibility=hidden ++LDFLAGS ?= -fvisibility=hidden + VERSION_SCRIPT_LDFLAGS = -Wl,-version-script,$(srcprefix)htslib.map + LIBS = $(htslib_default_libs) + +-prefix = /usr/local ++prefix = ${PREFIX} + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin + includedir = $(prefix)/include diff --git a/biology/ucsc-userapps/pkg-plist b/biology/ucsc-userapps/pkg-plist index 52e1fcc7fc79..b5270010ca7f 100644 --- a/biology/ucsc-userapps/pkg-plist +++ b/biology/ucsc-userapps/pkg-plist @@ -1,155 +1,157 @@ bin/kent bin/ucsc-shell userapps/bin/aNotB userapps/bin/addCols userapps/bin/ave userapps/bin/aveCols userapps/bin/bamToPsl userapps/bin/barChartMaxLimit userapps/bin/bedClip userapps/bin/bedCommonRegions userapps/bin/bedGeneParts userapps/bin/bedGraphPack userapps/bin/bedGraphToBigWig userapps/bin/bedJoinTabOffset userapps/bin/bedJoinTabOffset.py 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/bigGuessDb userapps/bin/bigHeat 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/chromToUcsc 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/expMatrixToBarchartBed 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/hubtools userapps/bin/jkUniq userapps/bin/lineCount userapps/bin/linesToRa userapps/bin/localtime userapps/bin/matrixClusterColumns userapps/bin/matrixMarketToTsv userapps/bin/matrixNormalize userapps/bin/matrixToBarChartBed 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/pslMap userapps/bin/pslMapPostChain userapps/bin/pslPosTarget userapps/bin/pslProtToRnaCoords userapps/bin/pslRc userapps/bin/pslRemoveFrameShifts userapps/bin/pslScore userapps/bin/pslSpliceJunctions userapps/bin/pslSwap userapps/bin/pslToPslx userapps/bin/pslToXa userapps/bin/raToLines userapps/bin/raToTab userapps/bin/randomLines userapps/bin/rmFaDups userapps/bin/rowsToCols 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/tabFmt userapps/bin/tabToMmHash userapps/bin/tableSum userapps/bin/tailLines userapps/bin/tdbRename userapps/bin/tdbSort 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/ucscApiClient userapps/bin/udcCleanup userapps/bin/undupFa userapps/bin/upper userapps/bin/vcfFilter userapps/bin/venn userapps/bin/verticalSplitSqlTable userapps/bin/webSync userapps/bin/weedLines userapps/bin/wigCorrelate userapps/bin/wigToBigWig userapps/bin/wordLine