Second run at cleaning out non staged ports without pending PR

5 files changed, 0 insertions, 69 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 14f7b8a61350..320b3cf71105 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -57,7 +57,6 @@
     SUBDIR += p5-bioperl
     SUBDIR += p5-bioperl-run
     SUBDIR += paml
-    SUBDIR += phd2fasta
     SUBDIR += phrap
     SUBDIR += phred
     SUBDIR += phylip
diff --git a/biology/phd2fasta/Makefile b/biology/phd2fasta/Makefile
deleted file mode 100644
index f45d9e8ed25b..000000000000
--- a/biology/phd2fasta/Makefile
+++ /dev/null
@@ -1,48 +0,0 @@
-# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
-# $FreeBSD$
-
-PORTNAME=	phd2fasta
-PORTVERSION=	0.990622.f
-CATEGORIES=	biology
-MASTER_SITES=	# put the tarball manually
-DISTFILES=	phd2fasta-acd-dist.tar.Z
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Converter from output files of Phred/Consed to FASTA files
-
-RESTRICTED=	Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
-.if defined(PACKAGE_BUILDING)
-IGNORE=		distribution files must be obtained via the authors
-.endif
-
-NO_WRKSUBDIR=	yes
-
-ALL_TARGET=	phd2fasta
-
-BINMODE=	0111	# avoid copying binaries as required by the agreement
-BINARIES=	phd2fasta
-PLIST_FILES=	bin/phd2fasta
-
-PORTDOCS=	PHD2FASTA.DOC
-
-NO_STAGE=	yes
-.include <bsd.port.pre.mk>
-
-.for f in ${DISTFILES}
-.if !exists(${DISTDIR}/${f})
-IGNORE=	you must request the source code (${f}) via e-mail, place it manually in ${DISTDIR}, and then try it again
-.endif
-.endfor
-
-do-install:
-.for f in ${BINARIES}
-	@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/
-.endfor
-.if ${PORT_OPTIONS:MDOCS}
-	@${MKDIR} ${DOCSDIR}
-.for f in ${PORTDOCS}
-	@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
-.endfor
-.endif
-
-.include <bsd.port.post.mk>
diff --git a/biology/phd2fasta/distinfo b/biology/phd2fasta/distinfo
deleted file mode 100644
index f2da8d1249ff..000000000000
--- a/biology/phd2fasta/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (phd2fasta-acd-dist.tar.Z) = e73e190a9721e8f459e8589bd448114cf670054240439dec2c8cde8d9f97c6a0
-SIZE (phd2fasta-acd-dist.tar.Z) = 58431
diff --git a/biology/phd2fasta/files/patch-Makefile b/biology/phd2fasta/files/patch-Makefile
deleted file mode 100644
index 3dd2d7f8d370..000000000000
--- a/biology/phd2fasta/files/patch-Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
---- Makefile.orig	2002-08-09 05:30:48.000000000 +0900
-+++ Makefile	2007-12-06 19:02:31.000000000 +0900
-@@ -1,5 +1,5 @@
--CC=cc
--CFLAGS=-O -w
-+CC?=cc
-+CFLAGS+=-w
- CLIB=-lm
- 
- OBJ= phd2fasta.o \
diff --git a/biology/phd2fasta/pkg-descr b/biology/phd2fasta/pkg-descr
deleted file mode 100644
index e965d0987bd0..000000000000
--- a/biology/phd2fasta/pkg-descr
+++ /dev/null
@@ -1,8 +0,0 @@
-Phred and consed write sequence and quality value information in
-'phd' output files. A phd file contains information in a header,
-the called bases, the base quality values, and the base call trace
-locations.  Phd2fasta reads phd files and writes sequence and quality
-value FASTA files, which phrap and cross_match need as input.
-(Consed needs phd files in order to obtain the base call locations.)
-
-WWW: http://www.phrap.org/phredphrapconsed.html