Add blat 33, a fast tool for local sequence similarity searches.

PR:		ports/93060
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>

6 files changed, 100 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index a16c682cf739..f8ecae099be7 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -13,6 +13,7 @@
     SUBDIR += blast
     SUBDIR += clustalw
     SUBDIR += coalesce
+    SUBDIR += blat
     SUBDIR += chemeq
     SUBDIR += crimap
     SUBDIR += distribfold
diff --git a/biology/blat/Makefile b/biology/blat/Makefile
new file mode 100644
index 000000000000..8e96c552e4d9
--- /dev/null
+++ b/biology/blat/Makefile
@@ -0,0 +1,57 @@
+# ex:ts=8
+# New ports collection makefile for:	blat
+# Date created:		08 Dec 2005
+# Whom:	      		Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	blat
+PORTVERSION=	33
+CATEGORIES=	biology
+MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
+DISTNAME=	${PORTNAME}Src${PORTVERSION}
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	A fast tool for local sequence similarity searches
+
+USE_ZIP=	yes
+USE_GMAKE=	yes
+USE_GCC=	3.4+
+MAKEFILE=	makefile
+WRKSRC=		${WRKDIR}/${PORTNAME}Src
+MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}"
+
+SUB_FILES=	pkg-message
+
+EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
+		pslPretty pslReps pslSort twoBitInfo twoBitToFa
+
+.include <bsd.port.pre.mk>
+
+post-patch:
+	@${MKDIR} ${WRKSRC}/bin/${MACHTYPE}
+	@${MKDIR} ${WRKSRC}/lib/${MACHTYPE}
+	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g' \
+		${WRKSRC}/inc/common.mk
+.if ${OSVERSION} <= 500000
+	@${REINPLACE_CMD} -e 's,strtof,\(float\) strtod,g' \
+		${WRKSRC}/lib/sqlNum.c
+.endif
+
+do-install:
+.for exe in ${EXECUTABLES}
+	${INSTALL_PROGRAM} ${WRKSRC}/bin/${MACHTYPE}/${exe} ${PREFIX}/bin
+.endfor
+	${MKDIR} ${DATADIR}/webBlat
+	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat
+	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
+.endif
+
+post-install:
+	@${CAT} ${PKGMESSAGE}
+
+.include <bsd.port.post.mk>
diff --git a/biology/blat/distinfo b/biology/blat/distinfo
new file mode 100644
index 000000000000..aa2a1eab4db8
--- /dev/null
+++ b/biology/blat/distinfo
@@ -0,0 +1,3 @@
+MD5 (blatSrc33.zip) = 5f9d3a4a88e57dfc435b5dd465209918
+SHA256 (blatSrc33.zip) = 4ca932721f529d815e64b51940c94d8136faec52c6b8bf8c3fcd3706337d9a29
+SIZE (blatSrc33.zip) = 1308517
diff --git a/biology/blat/files/pkg-message.in b/biology/blat/files/pkg-message.in
new file mode 100644
index 000000000000..f31a1930a57f
--- /dev/null
+++ b/biology/blat/files/pkg-message.in
@@ -0,0 +1,8 @@
+===============================================================================
+
+ A CGI script (webBlat) and instructions on how to set up a BLAT web server
+ have been installed in 
+ 
+ %%DATADIR%%
+
+===============================================================================
diff --git a/biology/blat/pkg-descr b/biology/blat/pkg-descr
new file mode 100644
index 000000000000..e6d996a232e2
--- /dev/null
+++ b/biology/blat/pkg-descr
@@ -0,0 +1,14 @@
+BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
+and cross-species protein alignments. BLAT is more accurate and 500
+times faster than popular existing tools for mRNA/DNA alignments and 50
+times faster for protein alignments at sensitivity settings typically
+used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
+-- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
+http://dx.doi.org/10.1101/gr.229202)
+
+BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
+genome (but not the genome itself) in memory. Since the index takes up a
+bit less than a gigabyte of RAM, BLAT can deliver high performance on a
+reasonably priced Linux box.
+
+WWW: http://www.genomeblat.com
diff --git a/biology/blat/pkg-plist b/biology/blat/pkg-plist
new file mode 100644
index 000000000000..d87a4966eeb8
--- /dev/null
+++ b/biology/blat/pkg-plist
@@ -0,0 +1,17 @@
+bin/blat
+bin/faToNib
+bin/faToTwoBit
+bin/gfClient
+bin/gfServer
+bin/nibFrag
+bin/pslPretty
+bin/pslReps
+bin/pslSort
+bin/twoBitInfo
+bin/twoBitToFa
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%DATADIR%%/webBlat/webBlat
+%%DATADIR%%/webBlat/install.txt
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%DATADIR%%/webBlat
+@dirrm %%DATADIR%%