# New ports collection makefile for:	fasta
# Date created:		29 January 2001
# Whom:	      		Johann Visagie <johann@egenetics.com>
#
# $FreeBSD$
#

PORTNAME=	fasta
PORTVERSION=	21.u1.d0
CATEGORIES=	biology
MASTER_SITES=	http://ftp.virginia.edu/pub/fasta/
DISTNAME=	fasta${PORTVERSION:S/.//g}
EXTRACT_SUFX=	.shar.Z

MAINTAINER=	ports@FreeBSD.org
COMMENT=	A collection of programs for searching DNA and protein databases

NO_CDROM=	May not be sold or incorporated into a commercial product
WRKSRC=		${WRKDIR}/fasta
PKGMESSAGE=	${WRKDIR}/pkg-message
FASTA_DOCS=	COPYRIGHT README.versions fasta20.doc fasta20.me format.doc \
		readme.*

MAN1=		align.1 fasta.1 lalign.1 prdf.1 prss.1 randseq.1 ssearch.1
MLINKS=		fasta.1 tfasta.1 fasta.1 lfasta.1 fasta.1 plfasta.1 \
		fasta.1 fastx.1  fasta.1 tfastx.1 \
		align.1 align0.1 lalign.1 plalign.1

do-extract:
	@ ${RM} -rf ${WRKDIR}
	@ ${MKDIR} ${WRKSRC}
	@ for file in ${EXTRACT_ONLY}; do \
	  cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \
	done

post-install:
.for manpage in ${MAN1}
	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
.endfor
.if !defined(NOPORTDOCS)
	@ ${MKDIR} ${DOCSDIR}
.for docfile in ${FASTA_DOCS}
	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
.endfor
.endif

.include <bsd.port.mk>
that still use it.  Bump PORTREVISION on their dependent
ports except the ones that depend on these:

audio/libogg
audio/libvorbis
devel/pcre
ftp/curl
graphics/jpeg
graphics/libart_lgpl
graphics/tiff
textproc/expat2
textproc/libxslt

In these cases the same trick as in the recent gettext update is used.
The ports install a symlink with the old library version.  When enough
of their dependent ports have had regular updates the remaining ones can
get a PORTREVISION bump and the links can be removed.

Also remove the devel/pcre dependency from USE_GNOME=glib20.  It causes
over 2200 packages to depend on devel/pcre while less than 200 actually
link with it.  The glib20 package still depends on devel/pcre so this
should not make a difference for ports with USE_GNOME=glib20.  Also,
libdata/pkgconfig/glib-2.0.pc lists pcre as a private library so
USE_GNOME=glib20 should not propagate it.

PR:		195724
Exp-run by:	antoine
Approved by:	portmgr (antoine)
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
the 32 ports that still use it.  Bump PORTREVISION on their dependent
ports except the ones that depend on these:

audio/libogg
audio/libvorbis
devel/pcre
ftp/curl
graphics/jpeg
graphics/libart_lgpl
graphics/tiff
textproc/expat2
textproc/libxslt

In these cases the same trick as in the recent gettext update is used.
The ports install a symlink with the old library version.  When enough
of their dependent ports have had regular updates the remaining ones can
get a PORTREVISION bump and the links can be removed.

Also remove the devel/pcre dependency from USE_GNOME=glib20.  It causes
over 2200 packages to depend on devel/pcre while less than 200 actually
link with it.  The glib20 package still depends on devel/pcre so this
should not make a difference for ports with USE_GNOME=glib20.  Also,
libdata/pkgconfig/glib-2.0.pc lists pcre as a private library so
USE_GNOME=glib20 should not propagate it.

PR:		195724
Exp-run by:	antoine
Approved by:	portmgr (antoine)
</pre>
</div>
</content>
</entry>
<entry>
<title>Update the default version of GCC in the Ports Collection from GCC 4.7.4</title>
<updated>2014-09-10T20:50:31+00:00</updated>
<author>
<name>gerald</name>
<email>gerald@FreeBSD.org</email>
</author>
<published>2014-09-10T20:50:31+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=c830042769f26309b16e0b0ace05fc30fec7b236'/>
<id>c830042769f26309b16e0b0ace05fc30fec7b236</id>
<content type='text'>
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
</pre>
</div>
</content>
</entry>
<entry>
<title>math/fftw3:</title>
<updated>2014-08-31T16:36:22+00:00</updated>
<author>
<name>tijl</name>
<email>tijl@FreeBSD.org</email>
</author>
<published>2014-08-31T16:36:22+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=8d3cbb81c0fa83b04e8805ac08f46e113648f4dd'/>
<id>8d3cbb81c0fa83b04e8805ac08f46e113648f4dd</id>
<content type='text'>
- Add USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Remove PTHREAD_CFLAGS and PTHREAD_LIBS
- Use MAKE_CMD
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
- Add USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Remove PTHREAD_CFLAGS and PTHREAD_LIBS
- Use MAKE_CMD
</pre>
</div>
</content>
</entry>
<entry>
<title>Remove indefinite articles and trailing periods from COMMENT, plus</title>
<updated>2014-06-13T07:36:27+00:00</updated>
<author>
<name>olgeni</name>
<email>olgeni@FreeBSD.org</email>
</author>
<published>2014-06-13T07:36:27+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=0f00c008b1cdb8e376be77e2a052866c6a025016'/>
<id>0f00c008b1cdb8e376be77e2a052866c6a025016</id>
<content type='text'>
minor COMMENT typos and surrounding whitespace fixes. Categories G-I.

CR:		D201
Approved by:	portmgr (bapt)
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
minor COMMENT typos and surrounding whitespace fixes. Categories G-I.

CR:		D201
Approved by:	portmgr (bapt)
</pre>
</div>
</content>
</entry>
<entry>
<title>- Fix build on HEAD (unknown clang option -malign-double)</title>
<updated>2014-04-04T10:14:34+00:00</updated>
<author>
<name>amdmi3</name>
<email>amdmi3@FreeBSD.org</email>
</author>
<published>2014-04-04T10:14:34+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=1f4f21c8689082d95a2cd03f1319c4aaa30051f9'/>
<id>1f4f21c8689082d95a2cd03f1319c4aaa30051f9</id>
<content type='text'>
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
</pre>
</div>
</content>
</entry>
<entry>
<title>- Remove DOCS, NLS and EXAMPLES from OPTIONS_DEFAULT in my ports, as suggested by Porter's Handbook</title>
<updated>2013-12-16T17:40:13+00:00</updated>
<author>
<name>amdmi3</name>
<email>amdmi3@FreeBSD.org</email>
</author>
<published>2013-12-16T17:40:13+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=26441a76abed38f0d11978cd4614fc35cdd01efc'/>
<id>26441a76abed38f0d11978cd4614fc35cdd01efc</id>
<content type='text'>
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
</pre>
</div>
</content>
</entry>
<entry>
<title>- Support staging</title>
<updated>2013-09-29T21:54:42+00:00</updated>
<author>
<name>amdmi3</name>
<email>amdmi3@FreeBSD.org</email>
</author>
<published>2013-09-29T21:54:42+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=c16115a0c49688d15eebae4d0d6ea583940671cd'/>
<id>c16115a0c49688d15eebae4d0d6ea583940671cd</id>
<content type='text'>
- Use new LIB_DEPENDS syntax
- Convert USE_GMAKE to USES
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
- Use new LIB_DEPENDS syntax
- Convert USE_GMAKE to USES
</pre>
</div>
</content>
</entry>
<entry>
<title>Add NO_STAGE all over the place in preparation for the staging support (cat: games)</title>
<updated>2013-09-20T17:36:33+00:00</updated>
<author>
<name>bapt</name>
<email>bapt@FreeBSD.org</email>
</author>
<published>2013-09-20T17:36:33+00:00</published>
<link rel='alternate' type='text/html' href='http://tfcis.org/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/?id=9ec8b69eee25166c3ea4802cd4645914c641361b'/>
<id>9ec8b69eee25166c3ea4802cd4645914c641361b</id>
<content type='text'>
</content>
<content type='xhtml'>
<div xmlns='http://www.w3.org/1999/xhtml'>
<pre>
</pre>
</div>
</content>
</entry>