diff options
author | Neil Blakey-Milner <nbm@FreeBSD.org> | 2000-07-28 13:16:10 +0000 |
---|---|---|
committer | Neil Blakey-Milner <nbm@FreeBSD.org> | 2000-07-28 13:16:10 +0000 |
commit | 167641b4f4961aaa7b26a7084250549a1ac4d096 (patch) | |
tree | 5dda80265502664ec9aa2d11b6e2308d2bcab94f /biology | |
parent | Update to 1.4. Also correct WWW while I'm here. (diff) |
Add p5-AcePerl, a perl interface to the ACEDB genome database system
PR: ports/20223
Submitted by: Johann Visagie <johann@egenetics.com>
Notes
Notes:
svn path=/head/; revision=31083
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/p5-AcePerl/Makefile | 37 | ||||
-rw-r--r-- | biology/p5-AcePerl/distinfo | 1 | ||||
-rw-r--r-- | biology/p5-AcePerl/files/FREEBSD_DEF | 23 | ||||
-rw-r--r-- | biology/p5-AcePerl/files/patch-aa | 22 | ||||
-rw-r--r-- | biology/p5-AcePerl/files/patch-ab | 11 | ||||
-rw-r--r-- | biology/p5-AcePerl/pkg-comment | 1 | ||||
-rw-r--r-- | biology/p5-AcePerl/pkg-descr | 8 | ||||
-rw-r--r-- | biology/p5-AcePerl/pkg-plist | 73 |
9 files changed, 177 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index d91b479913aa..e0504574c68f 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -11,6 +11,7 @@ SUBDIR += molden SUBDIR += mopac SUBDIR += ortep3 + SUBDIR += p5-AcePerl SUBDIR += paml SUBDIR += phylip SUBDIR += platon diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile new file mode 100644 index 000000000000..11e90f57696a --- /dev/null +++ b/biology/p5-AcePerl/Makefile @@ -0,0 +1,37 @@ +# New ports collection makefile for: p5-AcePerl +# Date created: 26 July 2000 +# Whom: Johann Visagie <johann@egenetics.com> +# +# $FreeBSD$ +# + +PORTNAME= AcePerl +PORTVERSION= 1.62 +CATEGORIES= biology databases perl5 +MASTER_SITES= http://stein.cshl.org/AcePerl/archive/ \ + ${MASTER_SITE_PERL_CPAN} +MASTER_SITE_SUBDIR=Ace +PKGNAMEPREFIX= p5- + +MAINTAINER= johann@egenetics.com + +USE_PERL5= YES + +MAN3= Ace::Sequence::Feature.3 \ + Ace::Sequence.3 \ + Ace.3 \ + Ace::Sequence::FeatureList.3 \ + Ace::Sequence::Multi.3 \ + Ace::Sequence::Homol.3 \ + Ace::Object.3 \ + Ace::Local.3 \ + Ace::Iterator.3 \ + Ace::Model.3 + +MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION} + +do-configure: + ${CP} ${FILESDIR}/FREEBSD_DEF ${WRKSRC}/ace/wmake/ + @ cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL + +.include <bsd.port.mk> diff --git a/biology/p5-AcePerl/distinfo b/biology/p5-AcePerl/distinfo new file mode 100644 index 000000000000..9f0e26a085ea --- /dev/null +++ b/biology/p5-AcePerl/distinfo @@ -0,0 +1 @@ +MD5 (AcePerl-1.62.tar.gz) = d9978077a8e1857b94216d5a28bc38ef diff --git a/biology/p5-AcePerl/files/FREEBSD_DEF b/biology/p5-AcePerl/files/FREEBSD_DEF new file mode 100644 index 000000000000..685175adcd87 --- /dev/null +++ b/biology/p5-AcePerl/files/FREEBSD_DEF @@ -0,0 +1,23 @@ +################################################################# +############### acedb: R.Durbin and J.Thierry-Mieg ############## +################################################################# + +################################################################# +########### This file is included by wmake/truemake ############# +###### Edit this file to adapt the ACeDB to a new machine ###### +##### following the explanations given in wmake/truemake ##### +################################################################# + +CFLAGS+= -g -Wall -O2 -DACEDB4 +NAME = FREEBSD +COMPILER = gcc ${CFLAGS} +LINKER = gcc -g + +LIBS = -lm +Xt_LIBS = -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11 +LEX_LIBS = + +RPCGEN_FLAGS = -b -I -K -1 + +################################################################# +################################################################# diff --git a/biology/p5-AcePerl/files/patch-aa b/biology/p5-AcePerl/files/patch-aa new file mode 100644 index 000000000000..add3f24ba66b --- /dev/null +++ b/biology/p5-AcePerl/files/patch-aa @@ -0,0 +1,22 @@ +--- ace/wh/mystdlib.h.orig Fri Jul 2 23:04:55 1999 ++++ ace/wh/mystdlib.h Thu Jul 27 17:20:19 2000 +@@ -161,7 +161,7 @@ + #endif + + #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \ +- defined(HP) || defined(WIN32) ++ defined(HP) || defined(WIN32) || defined(FREEBSD) + + #ifdef WIN32 + #include <mbctype.h> +--- ace/wh/mydirent.h.orig Mon Jan 11 01:51:40 1999 ++++ ace/wh/mydirent.h Thu Jul 27 17:20:41 2000 +@@ -55,7 +55,7 @@ + extern char *getwd(char *pathname) ; + #endif /* HP || SOLARIS || WIN32 */ + +-#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) ++#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined(FREEBSD) + #include <dirent.h> + typedef struct dirent MYDIRENT ; + #endif diff --git a/biology/p5-AcePerl/files/patch-ab b/biology/p5-AcePerl/files/patch-ab new file mode 100644 index 000000000000..2ad84954665b --- /dev/null +++ b/biology/p5-AcePerl/files/patch-ab @@ -0,0 +1,11 @@ +--- ace/memsubs.c.orig Mon Jan 11 02:01:29 1999 ++++ ace/memsubs.c Thu Jul 27 17:18:45 2000 +@@ -21,7 +21,7 @@ + #if defined(NEXT) || defined(HP) || defined(MACINTOSH) + extern void* malloc(mysize_t size) ; + #elif !defined(WIN32) +-#include <malloc.h> /* normal machines */ ++#include <stdlib.h> /* normal machines */ + #endif + + /********** primary type definition **************/ diff --git a/biology/p5-AcePerl/pkg-comment b/biology/p5-AcePerl/pkg-comment new file mode 100644 index 000000000000..ff9627c37254 --- /dev/null +++ b/biology/p5-AcePerl/pkg-comment @@ -0,0 +1 @@ +Perl interface to the ACEDB genome database system diff --git a/biology/p5-AcePerl/pkg-descr b/biology/p5-AcePerl/pkg-descr new file mode 100644 index 000000000000..b282dac21cd5 --- /dev/null +++ b/biology/p5-AcePerl/pkg-descr @@ -0,0 +1,8 @@ +AcePerl is an object-oriented Perl interface for the ACEDB genome database +system. It provides functionality for connecting to remote ACEDB databases, +performing queries, fetching ACE objects, and updating databases. + +WWW: http://stein.cshl.org/AcePerl/ + +- Johann +johann@egenetics.com diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist new file mode 100644 index 000000000000..0de06a9b8076 --- /dev/null +++ b/biology/p5-AcePerl/pkg-plist @@ -0,0 +1,73 @@ +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.bs +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.so +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Local.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Model.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF/Filehandle.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isTimestamp.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/find.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/ping.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/timestamps.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace |