biology/ucsc-userapps: Command line tools from the UCSC Genome Browser project

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.

biology/ucsc-userapps/Makefile

@@ -0,0 +1,76 @@
+# Created by: J. Bacon <jwb@FreeBSD.org>
+
+PORTNAME=	ucsc-userapps
+DISTVERSION=	413
+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\
+		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
+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 <bsd.port.mk>

biology/ucsc-userapps/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1619366655
+SHA256 (userApps.v413.src.tgz) = 91c51fec26bc61ea0dd9c4d0d13c76ce26e1c7d7f7dddbd3067c70beaec0af19
+SIZE (userApps.v413.src.tgz) = 19186621

biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c

@@ -0,0 +1,11 @@
+--- kent/src/hg/encode3/eap/eapFinish/eapFinish.c.orig	2021-04-14 11:23:30 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. */
+-#include <uuid/uuid.h>
++#include <uuid.h>
+ #include "common.h"
+ #include "linefile.h"
+ #include "hash.h"

biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c

@@ -0,0 +1,11 @@
+--- kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c.orig	2021-04-14 11:23:12 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. */
+-#include <uuid/uuid.h>
++#include <uuid.h>
+ #include "common.h"
+ #include "linefile.h"
+ #include "hash.h"

biology/ucsc-userapps/files/patch-kent_src_inc_common.mk

@@ -0,0 +1,13 @@
+--- kent/src/inc/common.mk.orig	2021-04-02 22:47:03 UTC
++++ kent/src/inc/common.mk
+@@ -61,6 +61,10 @@ else
+   endif
+ endif
+ 
++ifeq ($(UNAME_S),FreeBSD)
++  ICONVLIB=-L${LOCALBASE}/lib -liconv
++endif
++
+ # autodetect if openssl is installed
+ ifeq (${SSLDIR},)
+   SSLDIR = /usr/include/openssl

biology/ucsc-userapps/files/patch-kent_src_inc_uuid.h

@@ -0,0 +1,11 @@
+--- kent/src/inc/uuid.h.orig	2021-04-14 11:17:54 UTC
++++ kent/src/inc/uuid.h
+@@ -5,7 +5,7 @@
+  *
+  * If you use this file you need to add -luuid to your link line. */
+ 
+-#include <uuid/uuid.h>
++#include <uuid.h>
+ 
+ #define UUID_STRING_SIZE 37
+ 

biology/ucsc-userapps/files/patch-kent_src_lib_uuid.c

@@ -0,0 +1,11 @@
+--- kent/src/lib/uuid.c.orig	2021-04-14 11:22:38 UTC
++++ kent/src/lib/uuid.c
+@@ -6,7 +6,7 @@
+  * If you use this file you need to add -luuid to your link line. */
+ 
+ #include "common.h"
+-#include "uuid.h"
++#include "my_uuid.h"
+ 
+ char *makeUuidString(char buf[37])
+ /* Generate a random uuid and put it in the usual hex-plus-dashes form */

biology/ucsc-userapps/files/patch-kent_src_utils_dnsInfo_dnsInfo.c

@@ -0,0 +1,10 @@
+--- kent/src/utils/dnsInfo/dnsInfo.c.orig	2021-04-18 01:19:08 UTC
++++ kent/src/utils/dnsInfo/dnsInfo.c
+@@ -7,6 +7,7 @@
+ #include <netinet/in.h>
+ #include <arpa/inet.h>
+ #include <sys/utsname.h>
++#include <sys/socket.h>
+ #include "linefile.h"
+ #include "hash.h"
+ #include "options.h"

biology/ucsc-userapps/files/patch-kent_src_utils_dnsInfo_makefile

@@ -0,0 +1,11 @@
+--- kent/src/utils/dnsInfo/makefile.orig	2021-04-18 01:20:21 UTC
++++ kent/src/utils/dnsInfo/makefile
+@@ -1,7 +1,7 @@
+ kentSrc = ../..
+ include ../../inc/common.mk
+ 
+-L += -lm -lresolv
++L += -lm
+ MYLIBDIR = ../../lib/$(MACHTYPE)
+ MYLIBS =  $(MYLIBDIR)/jkweb.a
+ 

biology/ucsc-userapps/files/ucsc-shell.in

@@ -0,0 +1,28 @@
+#!/bin/sh -e
+
+ucsc_bin=%%PREFIX%%/userapps/bin
+cat << EOM
+
+Adding $ucsc_bin to \$PATH.
+
+UCSC kent utils contains commands that conflict with other tools, including
+at least "calc", "mktime", and "stringify".
+
+The other commands with these names may serve entirely different functions
+and will not be accessible while running this shell unless you refer to them
+by their absolute path name (e.g. /usr/local/bin/calc), which is not portable,
+BTW, so don't hard-code such paths into your scripts.
+
+Type "exit" or "Ctrl+D" to return to your normal shell.
+
+EOM
+
+export PATH=${ucsc_bin}:$PATH
+
+# FIXME: Update shell prompts to include (ucsc-kent)?
+
+# Invoke the user's chosen shell
+if echo $SHELL | egrep -q '/t?csh'; then
+    args='-f'
+fi
+exec $SHELL $args

biology/ucsc-userapps/pkg-descr

@@ -0,0 +1,8 @@
+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.
+
+WWW: http://hgdownload.cse.ucsc.edu/admin/exe/

biology/ucsc-userapps/pkg-message

@@ -0,0 +1,14 @@
+[
+{ type: install
+  message: <<EOM
+
+ucsc-kentutils is installed in it's own directory in order to avoid install
+conflicts with other ports.  Run "ucsc-shell" to gain access to ucsc-kentutils
+commands in your PATH.
+
+This port installs only freely available components of the UCSC userApps
+distribution.  See http://genome.ucsc.edu/license/ for more information.
+
+EOM
+}
+]

biology/ucsc-userapps/pkg-plist

@@ -0,0 +1,135 @@
+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/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