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Add p5-AcePerl, a perl interface to the ACEDB genome database system
PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com>
This commit is contained in:
Neil Blakey-Milner
parent
1f732231c2
commit
167641b4f4
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=31083
@ -11,6 +11,7 @@
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SUBDIR += molden
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SUBDIR += mopac
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SUBDIR += ortep3
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SUBDIR += p5-AcePerl
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SUBDIR += paml
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SUBDIR += phylip
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SUBDIR += platon
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37
biology/p5-AcePerl/Makefile
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37
biology/p5-AcePerl/Makefile
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@ -0,0 +1,37 @@
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# New ports collection makefile for: p5-AcePerl
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# Date created: 26 July 2000
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# Whom: Johann Visagie <johann@egenetics.com>
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#
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# $FreeBSD$
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#
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PORTNAME= AcePerl
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PORTVERSION= 1.62
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CATEGORIES= biology databases perl5
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MASTER_SITES= http://stein.cshl.org/AcePerl/archive/ \
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${MASTER_SITE_PERL_CPAN}
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MASTER_SITE_SUBDIR=Ace
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PKGNAMEPREFIX= p5-
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MAINTAINER= johann@egenetics.com
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USE_PERL5= YES
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MAN3= Ace::Sequence::Feature.3 \
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Ace::Sequence.3 \
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Ace.3 \
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Ace::Sequence::FeatureList.3 \
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Ace::Sequence::Multi.3 \
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Ace::Sequence::Homol.3 \
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Ace::Object.3 \
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Ace::Local.3 \
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Ace::Iterator.3 \
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Ace::Model.3
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MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION}
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do-configure:
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${CP} ${FILESDIR}/FREEBSD_DEF ${WRKSRC}/ace/wmake/
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@ cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL
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.include <bsd.port.mk>
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1
biology/p5-AcePerl/distinfo
Normal file
1
biology/p5-AcePerl/distinfo
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@ -0,0 +1 @@
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MD5 (AcePerl-1.62.tar.gz) = d9978077a8e1857b94216d5a28bc38ef
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23
biology/p5-AcePerl/files/FREEBSD_DEF
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23
biology/p5-AcePerl/files/FREEBSD_DEF
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@ -0,0 +1,23 @@
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#################################################################
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############### acedb: R.Durbin and J.Thierry-Mieg ##############
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#################################################################
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#################################################################
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########### This file is included by wmake/truemake #############
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###### Edit this file to adapt the ACeDB to a new machine ######
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##### following the explanations given in wmake/truemake #####
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#################################################################
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CFLAGS+= -g -Wall -O2 -DACEDB4
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NAME = FREEBSD
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COMPILER = gcc ${CFLAGS}
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LINKER = gcc -g
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LIBS = -lm
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Xt_LIBS = -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11
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LEX_LIBS =
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RPCGEN_FLAGS = -b -I -K -1
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#################################################################
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#################################################################
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22
biology/p5-AcePerl/files/patch-aa
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22
biology/p5-AcePerl/files/patch-aa
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@ -0,0 +1,22 @@
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--- ace/wh/mystdlib.h.orig Fri Jul 2 23:04:55 1999
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+++ ace/wh/mystdlib.h Thu Jul 27 17:20:19 2000
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@@ -161,7 +161,7 @@
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#endif
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#if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \
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- defined(HP) || defined(WIN32)
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+ defined(HP) || defined(WIN32) || defined(FREEBSD)
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#ifdef WIN32
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#include <mbctype.h>
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--- ace/wh/mydirent.h.orig Mon Jan 11 01:51:40 1999
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+++ ace/wh/mydirent.h Thu Jul 27 17:20:41 2000
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@@ -55,7 +55,7 @@
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extern char *getwd(char *pathname) ;
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#endif /* HP || SOLARIS || WIN32 */
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-#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP)
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+#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined(FREEBSD)
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#include <dirent.h>
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typedef struct dirent MYDIRENT ;
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#endif
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11
biology/p5-AcePerl/files/patch-ab
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11
biology/p5-AcePerl/files/patch-ab
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@ -0,0 +1,11 @@
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--- ace/memsubs.c.orig Mon Jan 11 02:01:29 1999
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+++ ace/memsubs.c Thu Jul 27 17:18:45 2000
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@@ -21,7 +21,7 @@
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#if defined(NEXT) || defined(HP) || defined(MACINTOSH)
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extern void* malloc(mysize_t size) ;
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#elif !defined(WIN32)
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-#include <malloc.h> /* normal machines */
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+#include <stdlib.h> /* normal machines */
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#endif
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/********** primary type definition **************/
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1
biology/p5-AcePerl/pkg-comment
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1
biology/p5-AcePerl/pkg-comment
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Perl interface to the ACEDB genome database system
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8
biology/p5-AcePerl/pkg-descr
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8
biology/p5-AcePerl/pkg-descr
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@ -0,0 +1,8 @@
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AcePerl is an object-oriented Perl interface for the ACEDB genome database
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system. It provides functionality for connecting to remote ACEDB databases,
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performing queries, fetching ACE objects, and updating databases.
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WWW: http://stein.cshl.org/AcePerl/
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- Johann
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johann@egenetics.com
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73
biology/p5-AcePerl/pkg-plist
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73
biology/p5-AcePerl/pkg-plist
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@ -0,0 +1,73 @@
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.bs
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.so
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Local.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Model.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF/Filehandle.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isTimestamp.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/find.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/ping.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/timestamps.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm
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lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object
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@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace
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