ports/172496: biology/blat: Update to version 35
KATO Tsuguru
tkato432 at yahoo.com
Thu Oct 31 19:40:06 UTC 2013
The following reply was made to PR ports/172496; it has been noted by GNATS.
From: KATO Tsuguru <tkato432 at yahoo.com>
To: bug-followup at FreeBSD.org
Cc:
Subject: Re: ports/172496: biology/blat: Update to version 35
Date: Fri, 1 Nov 2013 04:25:33 +0900
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Remake of the patch against current tree.
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diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
--- /usr/ports/biology/blat/Makefile 2013-09-22 01:13:54.000000000 +0900
+++ biology/blat/Makefile 2013-11-01 00:00:00.000000000 +0900
@@ -2,55 +2,68 @@
# $FreeBSD: head/biology/blat/Makefile 327709 2013-09-20 15:55:44Z bapt $
PORTNAME= blat
-PORTVERSION= 34
+PORTVERSION= 35
CATEGORIES= biology
-MASTER_SITES= http://www.soe.ucsc.edu/~kent/src/
+MASTER_SITES= http://hgwdev.cse.ucsc.edu/~kent/src/
DISTNAME= ${PORTNAME}Src${PORTVERSION}
MAINTAINER= ports at FreeBSD.org
COMMENT= Fast tool for local sequence similarity searches
+LIB_DEPENDS= libpng15.so:${PORTSDIR}/graphics/png
+
+OPTIONS_DEFINE= DOCS
+
+WRKSRC= ${WRKDIR}/${PORTNAME}Src
+
USE_ZIP= yes
+USE_OPENSSL= yes
USE_GMAKE= yes
MAKEFILE= makefile
-WRKSRC= ${WRKDIR}/${PORTNAME}Src
-MAKE_ENV+= HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
+MAKE_ENV= MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \
+ PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \
+ HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
+
+CPPFLAGS+= $$(libpng-config --I_opts)
+LDFLAGS+= $$(libpng-config --ldflags)
SUB_FILES= pkg-message
+PORTDOCS= README
+PLIST_FILES= ${EXECUTABLES:S,^,bin/,} \
+ lib/blat/webBlat/webBlat \
+ lib/blat/webBlat/install.txt
+PLIST_DIRS= lib/blat/webBlat \
+ lib/blat
+
EXECUTABLES= blat faToNib faToTwoBit gfClient gfServer nibFrag \
pslPretty pslReps pslSort twoBitInfo twoBitToFa
-PLIST_FILES+= ${EXECUTABLES:S,^,bin/,}
-PORTDOCS= README
-PORTDATA= *
-
-OPTIONS_DEFINE= DOCS
+.include <bsd.port.options.mk>
-NO_STAGE= yes
post-patch:
@${MKDIR} ${WRKSRC}/bin/${ARCH}
@${MKDIR} ${WRKSRC}/lib/${ARCH}
- @${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
- ${WRKSRC}/inc/common.mk
-
-.include <bsd.port.options.mk>
+ @${FIND} ${WRKSRC} -name "makefile" | ${XARGS} ${REINPLACE_CMD} -e \
+ 's|$${DESTDIR}||g'
+ @${REINPLACE_CMD} -e \
+ 's|cd |$$(MAKE) -C | ; \
+ s| &&.*||' ${WRKSRC}/makefile
+ @${REINPLACE_CMD} -e \
+ 's|^CC=|CC?=| ; \
+ s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk
do-install:
.for exe in ${EXECUTABLES}
- ${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${PREFIX}/bin
+ (cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} \
+ ${STAGEDIR}${PREFIX}/bin)
.endfor
- @${MKDIR} ${DATADIR}/webBlat
- ${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat
- ${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat
-.if ${PORT_OPTIONS:MDOCS}
- @${MKDIR} ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
-.endif
-
-post-install:
- @${ECHO_MSG}
- @${CAT} ${PKGMESSAGE}
- @${ECHO_MSG}
+ @${MKDIR} ${STAGEDIR}${PREFIX}/lib/blat/webBlat
+ (cd ${WRKSRC}/webBlat && ${INSTALL_PROGRAM} webBlat \
+ ${STAGEDIR}${PREFIX}/lib/blat/webBlat)
+ (cd ${WRKSRC}/webBlat && ${INSTALL_DATA} install.txt \
+ ${STAGEDIR}${PREFIX}/lib/blat/webBlat)
+ @${MKDIR} ${STAGEDIR}${DOCSDIR}
+ (cd ${WRKSRC} && ${INSTALL_DATA} README ${STAGEDIR}${DOCSDIR})
.include <bsd.port.mk>
diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
--- /usr/ports/biology/blat/distinfo 2013-06-21 03:53:41.000000000 +0900
+++ biology/blat/distinfo 2013-11-01 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
-SIZE (blatSrc34.zip) = 2142975
+SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab
+SIZE (blatSrc35.zip) = 1887567
diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
--- /usr/ports/biology/blat/files/pkg-message.in 2013-06-21 03:53:41.000000000 +0900
+++ biology/blat/files/pkg-message.in 2013-11-01 00:00:00.000000000 +0900
@@ -3,6 +3,6 @@
A CGI script (webBlat) and instructions on how to set up a BLAT web server
have been installed in
- %%DATADIR%%
+ %%PREFIX%%/lib/blat
===============================================================================
diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
--- /usr/ports/biology/blat/pkg-descr 2013-06-21 03:53:41.000000000 +0900
+++ biology/blat/pkg-descr 2013-11-01 00:00:00.000000000 +0900
@@ -1,9 +1,9 @@
-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.
+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
@@ -11,4 +11,4 @@
bit less than a gigabyte of RAM, BLAT can deliver high performance on a
reasonably priced Linux box.
-WWW: http://www.genomeblat.com
+WWW: http://users.soe.ucsc.edu/~kent/
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