FreeBSD Bugzilla – Attachment 144094 Details for
Bug 191336
[maintainer update] biology/phred biology/phrap biology/consed update to consed 27.0 with staging support
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[patch]
svn diff for biology/phrap
phrap.diff (text/plain), 4.03 KB, created by
Motomichi Matsuzaki
on 2014-06-24 11:21:18 UTC
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Description:
svn diff for biology/phrap
Filename:
MIME Type:
Creator:
Motomichi Matsuzaki
Created:
2014-06-24 11:21:18 UTC
Size:
4.03 KB
patch
obsolete
>Index: Makefile >=================================================================== >--- Makefile (revision 359067) >+++ Makefile (working copy) >@@ -2,10 +2,10 @@ > # $FreeBSD$ > > PORTNAME= phrap >-PORTVERSION= 0.990329 >+PORTVERSION= 1.090518 > CATEGORIES= biology > MASTER_SITES= # put the tarball manually >-DISTFILES= distrib.tar.Z >+DISTFILES= distrib.tar.gz > DIST_SUBDIR= ${PORTNAME} > > MAINTAINER= mzaki@m.u-tokyo.ac.jp >@@ -19,19 +19,14 @@ > NO_WRKSUBDIR= yes > > MAKEFILE= makefile >-ALL_TARGET= all manyreads >+ALL_TARGET= all > >-BINARIES= cluster cross_match cross_match.manyreads loco \ >- phrap phrap.longreads phrap.manyreads swat >+BINARIES= calf_merge cluster cross_match loco phrap swat > SCRIPTS= phrapview >-.for f in ${BINARIES} ${SCRIPTS} >-PLIST_FILES+= bin/${f} >-.endfor > >-PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq >+PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 mb_matrix penalty2 vector.seq > PORTDOCS= general.doc phrap.doc swat.doc > >-NO_STAGE= yes > .include <bsd.port.pre.mk> > > .for f in ${DISTFILES} >@@ -42,21 +37,18 @@ > > do-install: > .for f in ${BINARIES} >- @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/ >- @${CHMOD} a-r ${PREFIX}/bin/${f} # as required by the agreement >+ @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ > .endfor > .for f in ${SCRIPTS} >- @${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/ >+ @${INSTALL_SCRIPT} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ > .endfor >- @${MKDIR} ${DATADIR} >+ @${MKDIR} ${STAGEDIR}${DATADIR} > .for f in ${PORTDATA} >- @${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR} >+ @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR} > .endfor >-.if ${PORT_OPTIONS:MDOCS} >- @${MKDIR} ${DOCSDIR} >+ @${MKDIR} ${STAGEDIR}${DOCSDIR} > .for f in ${PORTDOCS} >- @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} >+ @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR} > .endfor >-.endif > > .include <bsd.port.post.mk> >Index: distinfo >=================================================================== >--- distinfo (revision 359067) >+++ distinfo (working copy) >@@ -1,2 +1,3 @@ >-SHA256 (phrap/distrib.tar.Z) = e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc >-SIZE (phrap/distrib.tar.Z) = 366163 >+MD5 (phrap/distrib.tar.gz) = 93ef3d1cca4d1a70ed16511d30a355ab >+SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665 >+SIZE (phrap/distrib.tar.gz) = 333159 >Index: files/patch-makefile >=================================================================== >--- files/patch-makefile (revision 359067) >+++ files/patch-makefile (working copy) >@@ -1,9 +1,9 @@ >---- makefile.orig 1999-03-11 15:13:20.000000000 +0900 >-+++ makefile 2007-12-11 13:19:39.000000000 +0900 >-@@ -23,8 +23,8 @@ >- #*****************************************************************************/ >- >+--- makefile.orig 2009-06-03 00:45:34.000000000 +0900 >++++ makefile 2010-02-12 18:05:23.000000000 +0900 >+@@ -25,8 +25,8 @@ > # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) >+ #CC= icc >+ #CFLAGS= -O2 -wd266,880 > -CC= cc > -CFLAGS= -O2 > +CC?= cc >@@ -11,17 +11,3 @@ > LFLAGS= -lm > > SWATOBJS= swat.o weibull.o >-@@ -55,11 +55,11 @@ >- >- manyreads: >- touch swat.h; >-- make CFLAGS="-O2 -DMANYREADS" phrap cross_match; >-+ make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match; >- mv phrap phrap.manyreads; >- mv cross_match cross_match.manyreads; >- touch swat.h; >-- make CFLAGS="-O2 -DLONGREADS" phrap; >-+ make CFLAGS="$(CFLAGS) -DLONGREADS" phrap; >- mv phrap phrap.longreads; >- touch swat.h; >- make phrap cross_match; >Index: pkg-plist >=================================================================== >--- pkg-plist (revision 0) >+++ pkg-plist (working copy) >@@ -0,0 +1,9 @@ >+@mode 111 >+bin/calf_merge >+bin/cluster >+bin/cross_match >+bin/loco >+bin/phrap >+bin/phrapview >+bin/swat >+@mode > >Property changes on: pkg-plist >___________________________________________________________________ >Added: fbsd:nokeywords >## -0,0 +1 ## >+yes >\ No newline at end of property >Added: svn:eol-style >## -0,0 +1 ## >+native >\ No newline at end of property >Added: svn:mime-type >## -0,0 +1 ## >+text/plain >\ No newline at end of property
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mzaki
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