ports/172496: biology/blat: Update to version 35
KATO Tsuguru
tkato432 at yahoo.com
Mon Oct 8 18:00:31 UTC 2012
>Number: 172496
>Category: ports
>Synopsis: biology/blat: Update to version 35
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Mon Oct 08 18:00:27 UTC 2012
>Closed-Date:
>Last-Modified:
>Originator: KATO Tsuguru
>Release: FreeBSD 7.4-RELEASE-p10 i386
>Organization:
>Environment:
>Description:
- Update to version 35
New file:
files/patch-makefile
Remove file:
pkg-plist
>How-To-Repeat:
>Fix:
diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
--- /usr/ports/biology/blat/Makefile 2012-10-01 23:45:16.000000000 +0900
+++ biology/blat/Makefile 2012-10-03 06:08:01.000000000 +0900
@@ -2,44 +2,65 @@
# $FreeBSD: ports/biology/blat/Makefile,v 1.8 2012/10/01 14:45:16 tabthorpe Exp $
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= A fast tool for local sequence similarity searches
+LIB_DEPENDS= png15:${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}"
+MAKE_JOBS_SAFE=yes
+
+CPPFLAGS+= $$(libpng-config --I_opts)
+LDFLAGS+= $$(libpng-config --ldflags)
SUB_FILES= pkg-message
+PORTDOCS= README
+PLIST_FILES= ${EXECUTABLES:S,^,bin/,} \
+ lib/blat/webBlat/webBlat \
+ lib/blat/webBlat/install.txt
+PLIST_DIRS= lib/blat/webBlat \
+ lib/blat
+
EXECUTABLES= blat faToNib faToTwoBit gfClient gfServer nibFrag \
pslPretty pslReps pslSort twoBitInfo twoBitToFa
+.include <bsd.port.options.mk>
+
post-patch:
@${MKDIR} ${WRKSRC}/bin/${ARCH}
@${MKDIR} ${WRKSRC}/lib/${ARCH}
- @${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
- ${WRKSRC}/inc/common.mk
+ @${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} ${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 ${DOCSDIR}
+ @${MKDIR} ${PREFIX}/lib/blat/webBlat
+ (cd ${WRKSRC}/webBlat \
+ && ${INSTALL_PROGRAM} webBlat ${PREFIX}/lib/blat/webBlat \
+ && ${INSTALL_DATA} install.txt ${PREFIX}/lib/blat/webBlat)
+.if ${PORT_OPTIONS:MDOCS}
+ @${MKDIR} ${DOCSDIR}
+ (cd ${WRKSRC} && ${INSTALL_DATA} README ${DOCSDIR})
.endif
-
-post-install:
@${CAT} ${PKGMESSAGE}
.include <bsd.port.mk>
diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
--- /usr/ports/biology/blat/distinfo 2011-03-19 21:29:29.000000000 +0900
+++ biology/blat/distinfo 2012-10-03 04:51:43.000000000 +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/patch-makefile biology/blat/files/patch-makefile
--- /usr/ports/biology/blat/files/patch-makefile 1970-01-01 09:00:00.000000000 +0900
+++ biology/blat/files/patch-makefile 2012-10-03 05:45:18.000000000 +0900
@@ -0,0 +1,36 @@
+--- makefile.orig 2012-08-14 09:15:05.000000000 +0900
++++ makefile 2012-10-03 05:40:34.000000000 +0900
+@@ -1,18 +1,19 @@
+ all:
+- cd lib && ${MAKE}
+- cd jkOwnLib && ${MAKE}
+- cd blat && $(MAKE)
+- cd gfClient && $(MAKE)
+- cd gfServer && $(MAKE)
+- cd hg/pslPretty && $(MAKE)
+- cd hg/pslReps && $(MAKE)
+- cd hg/pslSort && $(MAKE)
+- cd utils/nibFrag && $(MAKE)
+- cd utils/faToNib && $(MAKE)
+- cd utils/faToTwoBit && $(MAKE)
+- cd utils/twoBitToFa && $(MAKE)
+- cd utils/twoBitInfo && $(MAKE)
+- cd webBlat && $(MAKE)
++
++ $(MAKE) -C lib
++ $(MAKE) -C jkOwnLib
++ $(MAKE) -C blat
++ $(MAKE) -C gfClient
++ $(MAKE) -C gfServer
++ $(MAKE) -C hg/pslPretty
++ $(MAKE) -C hg/pslReps
++ $(MAKE) -C hg/pslSort
++ $(MAKE) -C utils/nibFrag
++ $(MAKE) -C utils/faToNib
++ $(MAKE) -C utils/faToTwoBit
++ $(MAKE) -C utils/twoBitToFa
++ $(MAKE) -C utils/twoBitInfo
++ $(MAKE) -C webBlat
+
+ clean:
+ rm -f */*.o */*/*.o lib/*/*.a
diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
--- /usr/ports/biology/blat/files/pkg-message.in 2006-03-15 19:26:12.000000000 +0900
+++ biology/blat/files/pkg-message.in 2012-10-03 04:55:04.000000000 +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 2006-03-15 19:26:11.000000000 +0900
+++ biology/blat/pkg-descr 2012-10-03 06:06:19.000000000 +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/
diff -urN /usr/ports/biology/blat/pkg-plist biology/blat/pkg-plist
--- /usr/ports/biology/blat/pkg-plist 2006-03-15 19:26:11.000000000 +0900
+++ biology/blat/pkg-plist 1970-01-01 09:00:00.000000000 +0900
@@ -1,17 +0,0 @@
-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%%
- at dirrm %%DATADIR%%/webBlat
- at dirrm %%DATADIR%%
>Release-Note:
>Audit-Trail:
>Unformatted:
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