Date: Thu, 7 Nov 2024 13:28:07 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: aaa110d4b8fe - main - biology/ucsc-userapps: Update to 472 Message-ID: <202411071328.4A7DS7sj019743@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=aaa110d4b8fe64383826e03507d1cd4753a607ed commit aaa110d4b8fe64383826e03507d1cd4753a607ed Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2024-11-07 13:17:36 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2024-11-07 13:17:36 +0000 biology/ucsc-userapps: Update to 472 Numerous fixes and enhancements since v414 Changes: https://github.com/ucscGenomeBrowser/kent/releases Reported by: fuz --- biology/ucsc-userapps/Makefile | 16 ++++++++------- biology/ucsc-userapps/distinfo | 6 +++--- ...h-kent_src_hg_encode3_eap_eapFinish_eapFinish.c | 4 ++-- ...use_edwWebRegisterScript_edwWebRegisterScript.c | 4 ++-- .../files/patch-kent_src_hg_lib_jksql.c | 14 +++++++++++++ .../files/patch-kent_src_inc_common.mk | 21 +++++++++---------- biology/ucsc-userapps/files/ucsc-shell.in | 0 biology/ucsc-userapps/pkg-descr | 1 - biology/ucsc-userapps/pkg-plist | 24 +++++++++++++++++++--- 9 files changed, 61 insertions(+), 29 deletions(-) diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index 3621160d0594..7ed02e4b69ce 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -1,9 +1,8 @@ PORTNAME= ucsc-userapps -DISTVERSION= 414 -PORTREVISION= 1 +DISTVERSION= 472 CATEGORIES= biology perl5 python MASTER_SITES= http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ -DISTNAME= userApps.v${PORTVERSION}.src +DISTNAME= userApps.v${DISTVERSION}.src MAINTAINER= jwb@FreeBSD.org COMMENT= Command line tools from the UCSC Genome Browser project @@ -21,11 +20,13 @@ ONLY_FOR_ARCHS= amd64 ONLY_FOR_ARCHS_REASON= uses _mm_popcnt_u64() function BUILD_DEPENDS= bash:shells/bash -LIB_DEPENDS= libiconv.so:converters/libiconv \ +LIB_DEPENDS= libmysqlclient.so:databases/mysql80-client \ + libunwind.so:devel/libunwind \ + libfreetype.so:print/freetype2 \ libpng.so:graphics/png RUN_DEPENDS= bash:shells/bash -USES= gmake localbase:ldflags mysql shebangfix perl5 python ssl tar:tgz +USES= gmake iconv localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz RESTRICTED= Redistribution is limited, see license @@ -36,7 +37,8 @@ SHEBANG_FILES= kent/src/checkUmask.sh \ kent/src/utils/tdbSort \ kent/src/utils/trackDbIndexBb/trackDbIndexBb \ kent/src/utils/ucscApiClient \ - kent/src/utils/webSync + kent/src/utils/webSync \ + kent/src/utils/bigGuessDb/bigGuessDb WRKSRC= ${WRKDIR}/userApps CFLAGS+= -fcommon @@ -49,7 +51,7 @@ SUB_FILES= ucsc-shell # code from the libraries per conversation with UCSC. Work to resolve this # is ongoing. do-build: - @${MV} ${WRKSRC}/kent/src/inc/uuid.h ${WRKSRC}/kent/src/inc/my_uuid.h + @(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}) diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo index cc2c9ed9a4e7..e5f22b962d6f 100644 --- a/biology/ucsc-userapps/distinfo +++ b/biology/ucsc-userapps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1621027743 -SHA256 (userApps.v414.src.tgz) = 36910b5c84ea613d4eb6ccb9572f3b34d929c5571578b1d91013391895638ab0 -SIZE (userApps.v414.src.tgz) = 19195157 +TIMESTAMP = 1730984296 +SHA256 (userApps.v472.src.tgz) = 26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2 +SIZE (userApps.v472.src.tgz) = 24378966 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 index f97872c005d2..9f2b33c711da 100644 --- 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 @@ -1,9 +1,9 @@ ---- kent/src/hg/encode3/eap/eapFinish/eapFinish.c.orig 2021-04-14 11:23:30 UTC +--- 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 README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ -#include <uuid/uuid.h> +#include <uuid.h> #include "common.h" diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c index cdd532d146eb..8c40a258cf40 100644 --- a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c +++ b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c @@ -1,9 +1,9 @@ ---- kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c.orig 2021-04-14 11:23:12 UTC +--- kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c.orig 2024-10-16 04:15:27 UTC +++ kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c @@ -2,7 +2,7 @@ /* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ -#include <uuid/uuid.h> +#include <uuid.h> #include "common.h" 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..e75057e7937c --- /dev/null +++ b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c @@ -0,0 +1,14 @@ +--- kent/src/hg/lib/jksql.c.orig 2024-10-16 04:15:27 UTC ++++ kent/src/hg/lib/jksql.c +@@ -1128,8 +1128,9 @@ if (sp->verifyServerCert && !sameString(sp->verifyServ + // If turned on this can defeat Man-In-The-Middle attacks. + if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0")) + { +- #if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000 +- mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED); ++ #if !defined(MARIADB_BASE_VERSION) && defined(MYSQL_VERSION_ID) && (MYSQL_VERSION_ID >= 80000) ++ int ssl_mode = SSL_MODE_REQUIRED; ++ mysql_options(conn, MYSQL_OPT_SSL_MODE, &ssl_mode); + #else + my_bool flag = TRUE; + 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 b083cbf175c9..c04678ded9e1 100644 --- a/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk +++ b/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk @@ -1,13 +1,12 @@ ---- kent/src/inc/common.mk.orig 2021-04-02 22:47:03 UTC +--- kent/src/inc/common.mk.orig 2024-10-16 04:15:27 UTC +++ kent/src/inc/common.mk -@@ -61,6 +61,10 @@ else +@@ -65,6 +65,9 @@ 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 - endif - -+ifeq ($(UNAME_S),FreeBSD) -+ ICONVLIB=-L${LOCALBASE}/lib -liconv -+endif -+ - # autodetect if openssl is installed - ifeq (${SSLDIR},) - SSLDIR = /usr/include/openssl diff --git a/biology/ucsc-userapps/files/ucsc-shell.in b/biology/ucsc-userapps/files/ucsc-shell.in old mode 100755 new mode 100644 diff --git a/biology/ucsc-userapps/pkg-descr b/biology/ucsc-userapps/pkg-descr index 05129f558f62..e3ad755eee45 100644 --- a/biology/ucsc-userapps/pkg-descr +++ b/biology/ucsc-userapps/pkg-descr @@ -2,5 +2,4 @@ These are the command-line bioinformatics utilities associated with the UCSC genome browser. Care has been taken to install only the freely available tools. However, the license information at https://genome.ucsc.edu/license/ is not entirely clear and we may add non-free utilities in the future. - Contact UCSC if you are using this port for commercial purposes. diff --git a/biology/ucsc-userapps/pkg-plist b/biology/ucsc-userapps/pkg-plist index f8605fc771d0..52e1fcc7fc79 100644 --- a/biology/ucsc-userapps/pkg-plist +++ b/biology/ucsc-userapps/pkg-plist @@ -5,12 +5,14 @@ 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 @@ -19,6 +21,8 @@ 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 @@ -33,6 +37,7 @@ userapps/bin/catDir userapps/bin/catUncomment userapps/bin/ccCp userapps/bin/chopFaLines +userapps/bin/chromToUcsc userapps/bin/clusterMatrixToBarChartBed userapps/bin/colTransform userapps/bin/convolve @@ -41,6 +46,7 @@ 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 @@ -83,6 +89,10 @@ 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 @@ -91,19 +101,22 @@ userapps/bin/nibSize userapps/bin/nt4Frag userapps/bin/paraFetch userapps/bin/paraSync -userapps/bin/pslLiftSubrangeBlat +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/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 @@ -114,8 +127,11 @@ userapps/bin/stringify userapps/bin/subChar userapps/bin/subColumn userapps/bin/subs +userapps/bin/tabToMmHash userapps/bin/tableSum userapps/bin/tailLines +userapps/bin/tdbRename +userapps/bin/tdbSort userapps/bin/textHist2 userapps/bin/textHistogram userapps/bin/tickToDate @@ -125,12 +141,14 @@ 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
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