Attachment 157380 Details for Bug 200603 – Patch to update biology/mafft to 7.221

Patch to update biology/mafft to 7.221

mafft-7.221.diff (text/plain), 2.69 KB, created by cartwright on 2015-06-02 20:05:00 UTC

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Creator: cartwright

Created: 2015-06-02 20:05:00 UTC

Size: 2.69 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 388198)
>+++ Makefile	(working copy)
>@@ -1,8 +1,8 @@
>-# Created by: Reed A. Cartwright <reed@cartwrig.ht>
>+# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
> # $FreeBSD$
> 
> PORTNAME=	mafft
>-PORTVERSION=	7.149
>+PORTVERSION=	7.221
> CATEGORIES=	biology
> MASTER_SITES=	http://mafft.cbrc.jp/alignment/software/
> DISTNAME=	${PORTNAME}-${PORTVERSION}-without-extensions-src
>@@ -19,7 +19,7 @@
> 
> USES=		gmake shebangfix tar:tgz
> 
>-SHEBANG_FILES=	core/mafftash_premafft.tmpl
>+SHEBANG_FILES=	core/mafftash_premafft.tmpl core/seekquencer_premafft.tmpl
> 
> LIBEXEC_FILES=	dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
> 		pair2hat3s multi2hat3s pairash addsingle splittbfast \
>@@ -26,7 +26,7 @@
> 		disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \
> 		countlen seq2regtable regtable2seq score getlag dndpre \
> 		setcore replaceu restoreu setdirection makedirectionlist version
>-PERL_LIBEXEC_FILES=	mafftash_premafft.pl
>+PERL_LIBEXEC_FILES=	mafftash_premafft.pl seekquencer_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 \
>Index: distinfo
>===================================================================
>--- distinfo	(revision 388198)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (mafft-7.149-without-extensions-src.tgz) = cfd909ee28afcc191f99c7ca37a507ddbefe9fbc416ef5692528c68a60c7b29a
>-SIZE (mafft-7.149-without-extensions-src.tgz) = 373846
>+SHA256 (mafft-7.221-without-extensions-src.tgz) = 6d9cdcc04684c8c8ff61888dffc0396b48c713e4519a99f54e04c4a7179d2776
>+SIZE (mafft-7.221-without-extensions-src.tgz) = 376075
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 388198)
>+++ pkg-plist	(working copy)
>@@ -41,6 +41,7 @@
> libexec/mafft/replaceu
> libexec/mafft/restoreu
> libexec/mafft/score
>+libexec/mafft/seekquencer_premafft.pl
> libexec/mafft/seq2regtable
> libexec/mafft/setcore
> libexec/mafft/setdirection
>@@ -53,13 +54,11 @@
> %%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

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Attachments on bug 200603: 157380 | 157381 | 157382