add gp

GP is a set of small utilities to manipulate DNA sequences

8 files changed, 163 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 880d5e36e467..52ca8f84d005 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -11,6 +11,7 @@
     SUBDIR += fasta3
     SUBDIR += fastdnaml
     SUBDIR += gaussian98
+    SUBDIR += gp
     SUBDIR += gperiodic
     SUBDIR += hmmer
     SUBDIR += kinemage
diff --git a/biology/gp/Makefile b/biology/gp/Makefile
new file mode 100644
index 000000000000..088119d8fec1
--- /dev/null
+++ b/biology/gp/Makefile
@@ -0,0 +1,36 @@
+# ex:ts=8
+# New ports collection makefile for:	gp
+# Date created:			Feb 28, 2001
+# Whom:				Ying-Chieh Liao <ijliao@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	gp
+PORTVERSION=	0.25
+CATEGORIES=	biology
+MASTER_SITES=	http://www.bioinformatics.org/genpak/download/
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	ijliao@FreeBSD.org
+
+LIB_DEPENDS=	gd.1:${PORTSDIR}/graphics/gd \
+		png.4:${PORTSDIR}/graphics/png
+
+USE_GMAKE=	yes
+
+MAN1=	Genpak.1 gp_acc.1 gp_cusage.1 gp_digest.1 gp_dimer.1 gp_findorf.1 \
+	gp_gc.1 gp_getseq.1 gp_matrix.1 gp_mkmtx.1 gp_pattern.1 gp_qs.1 \
+	gp_randseq.1 gp_seq2prot.1 gp_slen.1 gp_tm.1 gp_trimer.1 gp_primer.1
+
+.if !defined(NOPORTDOCS)
+INSTALL_TARGET=	install docs
+.endif
+
+post-patch:
+	@${PERL} -pi -e "s|%%PREFIX%%|${PREFIX}|g ; \
+		s|%%MANPREFIX%%|${MANPREFIX}|g ; \
+		s|%%DOCDIR%%|${PREFIX}/share/doc|g ; \
+		s|%%CFLAGS%%|${CFLAGS}|g" ${WRKSRC}/Makefile
+
+.include <bsd.port.mk>
diff --git a/biology/gp/distinfo b/biology/gp/distinfo
new file mode 100644
index 000000000000..1d640501a87b
--- /dev/null
+++ b/biology/gp/distinfo
@@ -0,0 +1 @@
+MD5 (gp-0.25.tgz) = 35bc282e2da3d5af24cf44ed01a04551
diff --git a/biology/gp/files/patch-Makefile b/biology/gp/files/patch-Makefile
new file mode 100644
index 000000000000..db0ffe3ad507
--- /dev/null
+++ b/biology/gp/files/patch-Makefile
@@ -0,0 +1,51 @@
+--- Makefile.orig	Tue Feb 13 22:41:12 2001
++++ Makefile	Wed Feb 28 01:01:15 2001
+@@ -5,15 +5,13 @@
+ ######################################################################
+ # Change the following to suit your needs
+ 
+-SHELL=/bin/bash
+-
+ # The directory root of your installation
+ # If you make a personal installation, change it to your home directory
+ # Default: /usr
+ # uncomment the following line to install to the default directories...
+ # TREE=/usr
+ # ...or the following line to install into your home directory:
+-TREE=$(HOME)
++TREE=%%PREFIX%%
+ 
+ # if you don't have the gd graphic library installed, you have to comment out or
+ # delete the following line. However, gp_map is such a nice program, so you
+@@ -25,7 +23,7 @@
+ BINDIR=$(TREE)/bin
+ 
+ # directory to install the manual pages
+-MANDIR=$(TREE)/man
++MANDIR=%%MANPREFIX%%/man
+ 
+ #directory to install the data directory
+ DATADIR=$(TREE)/lib
+@@ -36,11 +34,11 @@
+ # A catalog will be created: $(DOCDIR)/gp
+ # It will *not* be uninstalled automagically after a "make uninstall"
+ 
+-DOCDIR=$(TREE)/doc
++DOCDIR=%%DOCDIR%%
+ 
+ # Your favourite ANSI compiler and it's flags
+ CC=gcc
+-CFLAGS=-ansi -pedantic -O3 
++CFLAGS=%%CFLAGS%%
+ 
+ ######################################################################
+ # Do not change anything below this line
+@@ -58,7 +56,7 @@
+ 	mporfs.seq
+ 
+ all: 
+-	cd src ; make PROGRAMS="$(PROGRAMS)" GDPROGRAMS="$(GDPROGRAMS)" CC=$(CC) \
++	cd src ; gmake PROGRAMS="$(PROGRAMS)" GDPROGRAMS="$(GDPROGRAMS)" CC=$(CC) \
+ 		LIBS="$(LIBS)" CFLAGS="$(CFLAGS)" ; 
+ 	@echo -e "\nAll programs compiled. \nType 'make install' to install all programs."
+ 
diff --git a/biology/gp/files/patch-src::Makefile b/biology/gp/files/patch-src::Makefile
new file mode 100644
index 000000000000..345fb413bb5b
--- /dev/null
+++ b/biology/gp/files/patch-src::Makefile
@@ -0,0 +1,10 @@
+--- src/Makefile.orig	Wed Feb 28 01:01:24 2001
++++ src/Makefile	Wed Feb 28 01:01:31 2001
+@@ -5,7 +5,6 @@
+ ######################################################################
+ # Change the following to suit your needs
+ 
+-SHELL=/bin/bash
+ CC=gcc
+ LIBS= -lz -lm
+ #CFLAGS= -DNLS -DGZ
diff --git a/biology/gp/pkg-comment b/biology/gp/pkg-comment
new file mode 100644
index 000000000000..c8710a783594
--- /dev/null
+++ b/biology/gp/pkg-comment
@@ -0,0 +1 @@
+GP is a set of small utilities to manipulate DNA sequences
diff --git a/biology/gp/pkg-descr b/biology/gp/pkg-descr
new file mode 100644
index 000000000000..a8f362329a99
--- /dev/null
+++ b/biology/gp/pkg-descr
@@ -0,0 +1,9 @@
+GP is a set of small utilities written in ANSI C to manipulate DNA
+sequences in a Unix fashion, fit for combining within shell and cgi
+scripts.
+
+The sequences are usually in fasta format, that means the first line
+is the sequence name starting with ">", and the sequence comes in the
+next lines. The programs accept also gzipped sequence files.
+
+WWW: http://www.bioinformatics.org/genpak/#gp
diff --git a/biology/gp/pkg-plist b/biology/gp/pkg-plist
new file mode 100644
index 000000000000..07c9bb039bf9
--- /dev/null
+++ b/biology/gp/pkg-plist
@@ -0,0 +1,54 @@
+bin/gp_acc
+bin/gp_cusage
+bin/gp_digest
+bin/gp_dimer
+bin/gp_findorf
+bin/gp_gc
+bin/gp_getseq
+bin/gp_matrix
+bin/gp_mkmtx
+bin/gp_pars
+bin/gp_pattern
+bin/gp_primer
+bin/gp_qs
+bin/gp_randseq
+bin/gp_scan
+bin/gp_seq2prot
+bin/gp_shift
+bin/gp_slen
+bin/gp_tm
+bin/gp_trimer
+lib/genpak/ecoli.mtx
+lib/genpak/enzyme.enz
+lib/genpak/mporfs.seq
+lib/genpak/myco.cdn
+lib/genpak/sample.seq
+lib/genpak/standard.cdn
+@dirrm lib/genpak
+%%PORTDOCS%%share/doc/gp/CHANGES.TXT
+%%PORTDOCS%%share/doc/gp/INSTALL.TXT
+%%PORTDOCS%%share/doc/gp/LICENSE.TXT
+%%PORTDOCS%%share/doc/gp/Makefile
+%%PORTDOCS%%share/doc/gp/README.TXT
+%%PORTDOCS%%share/doc/gp/html/README.html
+%%PORTDOCS%%share/doc/gp/html/gp_acc.html
+%%PORTDOCS%%share/doc/gp/html/gp_cusage.html
+%%PORTDOCS%%share/doc/gp/html/gp_digest.html
+%%PORTDOCS%%share/doc/gp/html/gp_dimer.html
+%%PORTDOCS%%share/doc/gp/html/gp_findorf.html
+%%PORTDOCS%%share/doc/gp/html/gp_gc.html
+%%PORTDOCS%%share/doc/gp/html/gp_getseq.html
+%%PORTDOCS%%share/doc/gp/html/gp_map.html
+%%PORTDOCS%%share/doc/gp/html/gp_matrix.html
+%%PORTDOCS%%share/doc/gp/html/gp_mkmtx.html
+%%PORTDOCS%%share/doc/gp/html/gp_pattern.html
+%%PORTDOCS%%share/doc/gp/html/gp_primer.html
+%%PORTDOCS%%share/doc/gp/html/gp_qs.html
+%%PORTDOCS%%share/doc/gp/html/gp_randseq.html
+%%PORTDOCS%%share/doc/gp/html/gp_seq2prot.html
+%%PORTDOCS%%share/doc/gp/html/gp_slen.html
+%%PORTDOCS%%share/doc/gp/html/gp_tm.html
+%%PORTDOCS%%share/doc/gp/html/gp_trimer.html
+%%PORTDOCS%%share/doc/gp/html/index.html
+%%PORTDOCS%%@dirrm share/doc/gp/html
+%%PORTDOCS%%@dirrm share/doc/gp