9 files changed, 1174 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index a9e3ab465a60..3c4484cea3a9 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -17,6 +17,7 @@
     SUBDIR += boinc-simap
     SUBDIR += chemeq
     SUBDIR += clustalw
+    SUBDIR += consed
     SUBDIR += crimap
     SUBDIR += distribfold
     SUBDIR += dna-qc
diff --git a/biology/consed/Makefile b/biology/consed/Makefile
new file mode 100644
index 000000000000..15700c79f7bf
--- /dev/null
+++ b/biology/consed/Makefile
@@ -0,0 +1,104 @@
+# 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_XLIB=	yes
+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.
+
+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>
diff --git a/biology/consed/distinfo b/biology/consed/distinfo
new file mode 100644
index 000000000000..83c8c19c0179
--- /dev/null
+++ b/biology/consed/distinfo
@@ -0,0 +1,3 @@
+MD5 (consed_linux.tar.Z) = 35d508cfc308128ab85b04c65d968efd
+SHA256 (consed_linux.tar.Z) = ac9ce155ce46f7200accaa033c9b1ea1d8c071c68c2a82ab5f4b623d9ff6b117
+SIZE (consed_linux.tar.Z) = 27555099
diff --git a/biology/consed/files/patch-misc_mktrace.c b/biology/consed/files/patch-misc_mktrace.c
new file mode 100644
index 000000000000..99fa065b0bbf
--- /dev/null
+++ b/biology/consed/files/patch-misc_mktrace.c
@@ -0,0 +1,14 @@
+--- misc/mktrace/mktrace.c.orig	Tue Aug 31 03:14:17 2004
++++ misc/mktrace/mktrace.c	Wed Jul 13 16:31:28 2005
+@@ -70,9 +70,9 @@
+   else
+   {
+     printf( "enter FASTA filename: " );
+-    gets( ifnm );
++    fgets( ifnm, sizeof(ifnm), stdin );
+     printf( "enter output filename: " );
+-    gets( ofnm );
++    fgets( ofnm, sizeof(ofnm), stdin );
+   }
+ 
+   /*
diff --git a/biology/consed/files/patch-scripts_addReads2Consed.perl b/biology/consed/files/patch-scripts_addReads2Consed.perl
new file mode 100644
index 000000000000..094a7028a701
--- /dev/null
+++ b/biology/consed/files/patch-scripts_addReads2Consed.perl
@@ -0,0 +1,11 @@
+--- scripts/addReads2Consed.perl.orig	2007-09-26 04:02:19.000000000 +0900
++++ scripts/addReads2Consed.perl	2007-12-11 17:27:20.000000000 +0900
+@@ -71,7 +71,7 @@
+ $szVectorFile = $szConsedHome . "/lib/screenLibs/vector.seq";
+ 
+ # change this to reflect wherever you put the phred parameter file
+-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
++$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
+ 
diff --git a/biology/consed/files/patch-scripts_determineReadTypes.perl b/biology/consed/files/patch-scripts_determineReadTypes.perl
new file mode 100644
index 000000000000..70405b43cca2
--- /dev/null
+++ b/biology/consed/files/patch-scripts_determineReadTypes.perl
@@ -0,0 +1,11 @@
+--- scripts/determineReadTypes.perl.orig	Tue Aug 31 03:14:13 2004
++++ scripts/determineReadTypes.perl	Wed Jul 13 17:00:22 2005
+@@ -177,7 +177,7 @@
+ # you can remove or comment out this line when you are satisfied with
+ # your customized version of this file.
+ 
+-die "You must edit determineReadTypes.perl--please read README.txt that came with consed.  Look under INSTALLING CONSED.  Also look at the comments at the beginning of determineReadTypes.perl  Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
++#die "You must edit determineReadTypes.perl--please read README.txt that came with consed.  Look under INSTALLING CONSED.  Also look at the comments at the beginning of determineReadTypes.perl  Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
+ 
+ $szVersion = "001205";
+ 
diff --git a/biology/consed/files/patch-scripts_phredPhrap b/biology/consed/files/patch-scripts_phredPhrap
new file mode 100644
index 000000000000..5ac28e3d808a
--- /dev/null
+++ b/biology/consed/files/patch-scripts_phredPhrap
@@ -0,0 +1,36 @@
+--- scripts/phredPhrap.orig	2007-09-26 04:02:20.000000000 +0900
++++ scripts/phredPhrap	2007-12-11 17:32:27.000000000 +0900
+@@ -101,7 +101,7 @@
+ 
+ 
+ # change this to reflect wherever you put the phredpar.dat file
+-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
++$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
+ 
+@@ -207,7 +207,7 @@
+ $chromatDirPath = "../chromat_dir";
+ $phdDirPath = "../phd_dir";
+ 
+-$niceExe = "/bin/nice";
++$niceExe = "/usr/bin/nice";
+ $mvExe = "/bin/mv";
+ $lsExe = "/bin/ls";
+ $pwdExe = "/bin/pwd";
+@@ -568,11 +568,11 @@
+ 
+ # only uncomment the following 4 lines when you have customized 
+ # determineReadTypes.perl
+-#print "\n\n--------------------------------------------------------\n";
+-#print "Now running determineReadTypes.perl...\n";
+-#print "--------------------------------------------------------\n\n\n";
++print "\n\n--------------------------------------------------------\n";
++print "Now running determineReadTypes.perl...\n";
++print "--------------------------------------------------------\n\n\n";
+ 
+-#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
++!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
+ 
+ 
+ print "\n\n--------------------------------------------------------\n";
diff --git a/biology/consed/pkg-descr b/biology/consed/pkg-descr
new file mode 100644
index 000000000000..f0c1defcddd8
--- /dev/null
+++ b/biology/consed/pkg-descr
@@ -0,0 +1,4 @@
+Consed is a tool for viewing and editing sequence assemblies made by phrap,
+and includes Autofinish which will automatically choose finishing reads.
+
+WWW: http://www.phrap.org/consed/consed.html
diff --git a/biology/consed/pkg-plist.examples b/biology/consed/pkg-plist.examples
new file mode 100644
index 000000000000..5fc178a1cb63
--- /dev/null
+++ b/biology/consed/pkg-plist.examples
@@ -0,0 +1,990 @@
+share/examples/consed/assembly_view/edit_dir/.consedrc
+share/examples/consed/assembly_view/edit_dir/.consedrc_mini
+share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta
+share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta.log
+share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1
+share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1.aview
+share/examples/consed/assembly_view/edit_dir/doNotShowInAssemblyView.fof
+share/examples/consed/assembly_view/edit_dir/fragSizes.txt
+share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q102.x1.phd.1
+share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.x1.phd.1
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