# New ports collection makefile for:	phred
# Date created:		8 July 2005
# Whom:			Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
#
# $FreeBSD$
#

PORTNAME=	consed
PORTVERSION=	16.0
CATEGORIES=	biology
MASTER_SITES=	http://www.phrap.org/consed/distributions/${PORTVERSION}/
DISTNAME=	${PORTNAME}_linux
EXTRACT_SUFX=	.tar.Z

MAINTAINER=	mzaki@biol.s.u-tokyo.ac.jp
COMMENT=	A graphical tool for editing Phrap assemblies

RUN_DEPENDS=	phred:${PORTSDIR}/biology/phred \
		phrap:${PORTSDIR}/biology/phrap \
		phd2fasta:${PORTSDIR}/biology/phd2fasta

USE_PERL5=	yes
USE_LINUX=	yes
USE_LINUX_APPS=	xorglibs
ONLY_FOR_ARCHS=	i386 amd64

RESTRICTED=	Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
.if defined(PACKAGE_BUILDING)
IGNORE=		distribution files must be obtained via the authors
.endif

NO_WRKSUBDIR=	yes

BUILD_WRKSRC=	${WRKSRC}/misc/mktrace
ALL_TARGET=	mktrace

BINARIES=	consed mktrace sffinfo sff2scf
CONTRIBS=	ace2OligosWithComments.perl ace2fof \
		aceContigs2Phds.perl acestatus.pl export_cons \
		mergeAces.perl recover_consensus_tags revert_fof
SCRIPTS=	ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \
		amplifyTranscripts.perl catPhdFiles.perl \
		countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \
		findSequenceMatchesForConsed.perl lib2Phd.perl \
		orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \
		revertToUneditedRead tagRepeats.perl transferConsensusTags.perl
.for f in ${BINARIES} ${CONTRIBS} ${SCRIPTS}
PLIST_FILES+=	bin/${f}
.endfor

DATADIR=	${PREFIX}/lib/screenLibs
DATAFILES=	primerCloneScreen.seq primerSubcloneScreen.seq \
		repeats.fasta singleVectorForRestrictionDigest.fasta
NULLFILES=	vector.seq
.for f in ${DATAFILES} ${NULLFILES}
PORTDATA+=	${f}.dist
.endfor
PORTDOCS=	README.txt

.if defined(WITH_EXAMPLES)
EXAMPLES=	standard autofinish assembly_view polyphred
PLIST=		${PKGDIR}/pkg-plist.examples
.endif

post-build:
	(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo)
	(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf)

do-install:
	@${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed
	@${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/
	@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/
	@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/
.for f in ${BINARIES}
	@${CHMOD} a-r ${PREFIX}/bin/${f}
.endfor
.for f in ${CONTRIBS}
	@${INSTALL_SCRIPT} ${WRKSRC}/contributions/${f} ${PREFIX}/bin/
.endfor
.for f in ${SCRIPTS}
	@${INSTALL_SCRIPT} ${WRKSRC}/scripts/${f} ${PREFIX}/bin/
.endfor
	@${MKDIR} ${DATADIR}
.for f in ${DATAFILES}
	@${INSTALL_DATA} ${WRKSRC}/misc/${f} ${DATADIR}/${f}.dist
.endfor
.for f in ${NULLFILES}
	@${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist
.endfor
.if !defined(NOPORTEXAMPLES)
	@${MKDIR} ${EXAMPLESDIR}
.for dir in ${EXAMPLES}
	@${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR}
.endfor
.endif
.if !defined(NOPORTDOCS)
	@${MKDIR} ${DOCSDIR}
.for f in ${PORTDOCS}
	@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
.endfor
.endif
.if !defined(WITH_EXAMPLES)
	@${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them."
.endif
	@${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'"

.include <bsd.port.mk>
/electron6/files/elliptic-6.5.4'>dependabot/npm_and_yarn/devel/electron6/files/elliptic-6.5.4</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/ini-1.3.8'>dependabot/npm_and_yarn/devel/electron6/files/ini-1.3.8</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/lodash-4.17.19'>dependabot/npm_and_yarn/devel/electron6/files/lodash-4.17.19</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/lodash.merge-4.6.2'>dependabot/npm_and_yarn/devel/electron6/files/lodash.merge-4.6.2</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/node-fetch-2.6.1'>dependabot/npm_and_yarn/devel/electron6/files/node-fetch-2.6.1</option>
<option value='dependabot/npm_and_yarn/devel/electron6/files/serve-10.1.2'>dependabot/npm_and_yarn/devel/electron6/files/serve-10.1.2</option>
<option value='gnome-3.22'>gnome-3.22</option>
<option value='gnome-3.24'>gnome-3.24</option>
<option value='gnome-3.26'>gnome-3.26</option>
<option value='gnome-3.28'>gnome-3.28</option>
<option value='gnome-3.32'>gnome-3.32</option>
<option value='gnome-3.36'>gnome-3.36</option>
<option value='gstreamer'>gstreamer</option>
<option value='gstreamer-1.16'>gstreamer-1.16</option>
<option value='gstreamer0.10-removal' selected='selected'>gstreamer0.10-removal</option>
<option value='main'>main</option>
<option value='master'>master</option>
<option value='mate-1.16'>mate-1.16</option>
<option value='mate-1.18'>mate-1.18</option>
<option value='mate-1.20'>mate-1.20</option>
<option value='mate-1.22'>mate-1.22</option>
</select> <input type='submit' value='switch'/></form></td></tr>
<tr><td class='sub'>FreeBSD GNOME current development ports (https://github.com/freebsd/freebsd-ports-gnome)</td><td class='sub right'></td></tr></table>
<table class='tabs'><tr><td>
<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/about/?h=gstreamer0.10-removal'>about</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/?h=gstreamer0.10-removal'>summary</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/refs/?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>refs</a><a class='active' href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/audio/gkrellmvolume2?h=gstreamer0.10-removal'>log</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/tree/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>tree</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>commit</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/diff/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>diff</a><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/stats/audio/gkrellmvolume2?h=gstreamer0.10-removal'>stats</a></td><td class='form'><form class='right' method='get' action='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/audio/gkrellmvolume2'>
<input type='hidden' name='h' value='gstreamer0.10-removal'/><input type='hidden' name='id' value='601e9a288c99afee45fae05a24bb13101af37061'/><select name='qt'>
<option value='grep'>log msg</option>
<option value='author'>author</option>
<option value='committer'>committer</option>
<option value='range'>range</option>
</select>
<input class='txt' type='search' size='10' name='q' value=''/>
<input type='submit' value='search'/>
</form>
</td></tr></table>
<div class='path'>path: <a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>root</a>/<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/audio?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>audio</a>/<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061'>gkrellmvolume2</a></div><div class='content'><table class='list nowrap'><tr class='nohover'><th></th><th class='left'>Commit message (<a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/log/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=601e9a288c99afee45fae05a24bb13101af37061&amp;showmsg=1'>Expand</a>)</th><th class='left'>Author</th><th class='left'>Age</th><th class='left'>Files</th><th class='left'>Lines</th></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=01a85edfc4f084a2b56a64bd803f04202cde364f'>Though recent FreeBSD has SOUND_MIXER_INFO defined. it seems</a></td><td>ume</td><td><span title='2003-09-27 12:02:24 +0800'>2003-09-27</span></td><td>2</td><td><span class='deletions'>-0</span>/<span class='insertions'>+15</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=f36a66ae2921375aed546f693c78e94db4a4ef15'>Update to 2.1.8.</a></td><td>ume</td><td><span title='2003-06-18 01:49:11 +0800'>2003-06-18</span></td><td>2</td><td><span class='deletions'>-2</span>/<span class='insertions'>+2</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=12476c2aeffe5591591b1322f333d852413d9c7f'>De-pkg-comment.</a></td><td>ume</td><td><span title='2003-02-21 04:10:05 +0800'>2003-02-21</span></td><td>2</td><td><span class='deletions'>-1</span>/<span class='insertions'>+1</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=f22b54d9aec3c8c375e8d7bb7872d84211776fdb'>Update to 2.1.7.</a></td><td>ume</td><td><span title='2003-01-29 02:31:00 +0800'>2003-01-29</span></td><td>3</td><td><span class='deletions'>-2</span>/<span class='insertions'>+4</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=9fe24075962bc9724b2b34828233a54e052fae48'>Update to 2.1.5.</a></td><td>ume</td><td><span title='2002-11-07 04:10:50 +0800'>2002-11-07</span></td><td>4</td><td><span class='deletions'>-8</span>/<span class='insertions'>+17</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=0dd42ee1ce6247d1970baa3e4a6029219e0637ab'>Update to 2.1.4.</a></td><td>ume</td><td><span title='2002-10-06 03:47:25 +0800'>2002-10-06</span></td><td>3</td><td><span class='deletions'>-50</span>/<span class='insertions'>+3</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=aac13aa224b11f1e1b33d11f956523cf480a6c2d'>Update gkrellm-volume to 2.0.1 after repocopy.</a></td><td>ume</td><td><span title='2002-09-03 02:30:53 +0800'>2002-09-03</span></td><td>7</td><td><span class='deletions'>-57</span>/<span class='insertions'>+70</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=c09dc513f70813fd1915b12787ca0e934c4e4f5d'>Use USE_GNOMENG.</a></td><td>marcus</td><td><span title='2002-08-31 08:13:25 +0800'>2002-08-31</span></td><td>1</td><td><span class='deletions'>-1</span>/<span class='insertions'>+2</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=a0f5a8c8a9c459b81cad72a1706dcb7ee2e36bd1'>Make compilable under 5-CURRENT.</a></td><td>ume</td><td><span title='2002-06-29 17:04:46 +0800'>2002-06-29</span></td><td>1</td><td><span class='deletions'>-0</span>/<span class='insertions'>+14</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=48a4c1438b7d3ef0b9109df031219cddf60148f3'>Style: use tabs, not spaces, to indent variables in Makefiles.</a></td><td>olgeni</td><td><span title='2001-02-05 05:12:59 +0800'>2001-02-05</span></td><td>1</td><td><span class='deletions'>-1</span>/<span class='insertions'>+1</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=a6052314285b1dbfa58d2262078134dfe7292884'>Update to 0.8.</a></td><td>ume</td><td><span title='2001-01-14 23:15:04 +0800'>2001-01-14</span></td><td>2</td><td><span class='deletions'>-2</span>/<span class='insertions'>+4</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=3c9fabfa6dd4202d012476761268d276b4bb08f3'>Update to 0.7.</a></td><td>ume</td><td><span title='2000-10-27 18:26:52 +0800'>2000-10-27</span></td><td>2</td><td><span class='deletions'>-2</span>/<span class='insertions'>+2</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=cea38f8422a3eeac06b3ce4a5828580a5812d2cc'>Implement WANT_IMLIB and USE_IMLIB.</a></td><td>reg</td><td><span title='2000-10-05 14:57:56 +0800'>2000-10-05</span></td><td>1</td><td><span class='deletions'>-5</span>/<span class='insertions'>+1</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=17e088dda92f138b8bbb3ca83359d3e2657e3253'>Make sure to have plugin directory.</a></td><td>ume</td><td><span title='2000-06-26 23:41:42 +0800'>2000-06-26</span></td><td>1</td><td><span class='deletions'>-2</span>/<span class='insertions'>+8</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=1aca496a9e3b48453346cceec963f31e579f23d7'>Use X11BASE instead of PREFIX for BUILD_DEPENDS and remove unneeded PREFIX</a></td><td>sobomax</td><td><span title='2000-06-26 17:01:00 +0800'>2000-06-26</span></td><td>1</td><td><span class='deletions'>-2</span>/<span class='insertions'>+2</span></td></tr>
<tr><td class='commitgraph'>* </td><td><a href='/~lantw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/audio/gkrellmvolume2?h=gstreamer0.10-removal&amp;id=f5655e8ed2905034eead37cb2a00ca3619e7cfc2'>Initial import of gkrellmvolume.</a></td><td>ume</td><td><span title='2000-06-23 02:16:28 +0800'>2000-06-23</span>