ports/189746: [maintainer update] Update biology/mafft
Reed A. Cartwright
cartwright at asu.edu
Tue May 13 02:40:00 UTC 2014
>Number: 189746
>Category: ports
>Synopsis: [maintainer update] Update biology/mafft
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Tue May 13 02:40:00 UTC 2014
>Closed-Date:
>Last-Modified:
>Originator: Reed A. Cartwright
>Release: FreeBSD 10.0-RELEASE-p2 amd64
>Organization:
ASU
>Environment:
System: FreeBSD herschel.biodesign.asu.edu 10.0-RELEASE-p2 FreeBSD 10.0-RELEASE-p2 #0: Tue Apr 29 17:06:01 UTC 2014 root at amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64
>Description:
Update biology/mafft to 7.149 and support staging
>How-To-Repeat:
>Fix:
Patch is attached
--- mafft.diff begins here ---
Index: Makefile
===================================================================
--- Makefile (revision 353911)
+++ Makefile (working copy)
@@ -1,8 +1,8 @@
-# Created by: Fernan Aguero <fernan at iib.unsam.edu.ar>
+# Created by: Reed A. Cartwright <reed at cartwrig.ht>
# $FreeBSD$
PORTNAME= mafft
-PORTVERSION= 6.903
+PORTVERSION= 7.149
CATEGORIES= biology
MASTER_SITES= http://mafft.cbrc.jp/alignment/software/
DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src
@@ -11,28 +11,27 @@
MAINTAINER= cartwright at asu.edu
COMMENT= Multiple alignment program for amino acid or nucleotide sequences
-LICENSE= BSD
+LICENSE= BSD2CLAUSE
-RUN_DEPENDS= lav2ps:${PORTSDIR}/biology/fasta3
-
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions
BUILD_WRKSRC= ${WRKSRC}/core
-USES= gmake
+USES= gmake shebangfix
-MAN1= mafft.1 mafft-homologs.1
+SHEBANG_FILES= core/mafftash_premafft.tmpl
LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
- pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \
+ pair2hat3s multi2hat3s pairash addsingle splittbfast \
disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \
- countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \
+ countlen seq2regtable regtable2seq score getlag dndpre \
setcore replaceu restoreu setdirection makedirectionlist version
+PERL_LIBEXEC_FILES= mafftash_premafft.pl
SCRIPT_FILES= mafft mafft-homologs.rb
LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \
mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \
mafft-qinsi mafft-xinsi nwns nwnsi
+MAN1_FILES= mafft.1 mafft-homologs.1
-NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "sparc64"
@@ -48,27 +47,28 @@
${BUILD_WRKSRC}/Makefile
do-install:
- @${MKDIR} ${PREFIX}/libexec/${PORTNAME}
+ @${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
.for exec in ${LIBEXEC_FILES}
- ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME}
+ ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
.endfor
+.for exec in ${PERL_LIBEXEC_FILES}
+ ${INSTALL_SCRIPT} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
+.endfor
.for exec in ${SCRIPT_FILES}
- ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin
+ ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${STAGEDIR}${PREFIX}/bin
.endfor
.for exec in ${LN_FILES}
- ${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${exec}
+ ${LN} -sf mafft ${STAGEDIR}${PREFIX}/bin/${exec}
.endfor
- ${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-distance ${PREFIX}/bin/mafft-distance
- ${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-profile ${PREFIX}/bin/mafft-profile
-.for man in ${MAN1}
- ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${MAN1PREFIX}/man/man1
+ ${LN} -sf ../libexec/${PORTNAME}/mafft-distance ${STAGEDIR}${PREFIX}/bin/mafft-distance
+ ${LN} -sf ../libexec/${PORTNAME}/mafft-profile ${STAGEDIR}${PREFIX}/bin/mafft-profile
+.for man in ${MAN1_FILES}
+ ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${STAGEDIR}${MAN1PREFIX}/man/man1
.endfor
- @${MKDIR} ${EXAMPLESDIR}
- ${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR}
-.if ${PORT_OPTIONS:MDOCS}
- @${MKDIR} ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR}
-.endif
+ @${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+ ${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR}
+ @${MKDIR} ${STAGEDIR}${DOCSDIR}
+ ${INSTALL_DATA} ${WRKSRC}/readme ${STAGEDIR}${DOCSDIR}
+ ${INSTALL_DATA} ${WRKSRC}/license ${STAGEDIR}${DOCSDIR}
.include <bsd.port.post.mk>
Index: distinfo
===================================================================
--- distinfo (revision 353911)
+++ distinfo (working copy)
@@ -1,2 +1,2 @@
-SHA256 (mafft-6.903-without-extensions-src.tgz) = d96326aecdb1f86b63779312c4a6d8f719f32786396567c1d1829341fc6dbcc8
-SIZE (mafft-6.903-without-extensions-src.tgz) = 359536
+SHA256 (mafft-7.149-without-extensions-src.tgz) = cfd909ee28afcc191f99c7ca37a507ddbefe9fbc416ef5692528c68a60c7b29a
+SIZE (mafft-7.149-without-extensions-src.tgz) = 373846
Index: pkg-plist
===================================================================
--- pkg-plist (revision 353911)
+++ pkg-plist (working copy)
@@ -25,12 +25,12 @@
libexec/mafft/dndblast
libexec/mafft/dndfast7
libexec/mafft/dndpre
-libexec/mafft/dndpre2
libexec/mafft/dvtditr
libexec/mafft/f2cl
libexec/mafft/getlag
libexec/mafft/mafft-distance
libexec/mafft/mafft-profile
+libexec/mafft/mafftash_premafft.pl
libexec/mafft/makedirectionlist
libexec/mafft/mccaskillwrap
libexec/mafft/multi2hat3s
@@ -40,7 +40,6 @@
libexec/mafft/regtable2seq
libexec/mafft/replaceu
libexec/mafft/restoreu
-libexec/mafft/rnatest
libexec/mafft/score
libexec/mafft/seq2regtable
libexec/mafft/setcore
@@ -49,14 +48,18 @@
libexec/mafft/splittbfast
libexec/mafft/tbfast
libexec/mafft/version
+man/man1/mafft-homologs.1.gz
+man/man1/mafft.1.gz
%%PORTDOCS%%%%DOCSDIR%%/license
%%PORTDOCS%%%%DOCSDIR%%/readme
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.allowshift
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi.allowshift
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree
@@ -63,6 +66,6 @@
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
- at dirrm libexec/mafft
+ at dirrmtry libexec/mafft
+%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
+%%PORTEXAMPLES%%@dirrmtry %%EXAMPLESDIR%%
--- mafft.diff ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
More information about the freebsd-ports-bugs
mailing list