A new port garlic, free molecular viewer and editor, free molecular

visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.

6 files changed, 399 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 8f6463f959df..90d97ee596de 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -20,6 +20,7 @@
     SUBDIR += fastdnaml
     SUBDIR += flip
     SUBDIR += fluctuate
+    SUBDIR += garlic
     SUBDIR += genpak
     SUBDIR += gff2ps
     SUBDIR += gperiodic
diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile
new file mode 100644
index 000000000000..91a99b83bd43
--- /dev/null
+++ b/biology/garlic/Makefile
@@ -0,0 +1,59 @@
+# New ports collection makefile for:    garlic
+# Date created:         28 July 2003
+# Whom:                 maho@FreeBSD.org
+#
+# $FreeBSD$
+#
+
+PORTNAME=	garlic
+PORTVERSION=	1.4
+CATEGORIES=	biology
+MASTER_SITES=	http://garlic.mefos.hr/sources/garlic-${PORTVERSION}/
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
+.if !defined(NOPORTDOCS)
+DISTFILES+=	${DISTNAME}-doc${EXTRACT_SUFX}
+.endif
+EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
+
+MAINTAINER=	maho@FreeBSD.org
+COMMENT=	Molecular viewer, editor and visualization program
+
+USE_REINPLACE=  yes
+USE_GMAKE=	yes
+ALL_TARGET=     # empty
+
+.if defined(WITH_OPTIMIZED_FLAGS)
+CFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double
+.if (${MACHINE_ARCH} == "i386")
+CFLAGS+=	-mcpu=i686 -march=i686 -mfancy-math-387
+.endif # i386
+.endif
+
+post-patch:
+	@${REINPLACE_CMD} -e 's|%%X11BASE%%|${X11BASE}|g ; \
+	s|%%LOCALBASE%%|${LOCALBASE}|g ;\
+	s|%%CC%%|${CC}|g ; \
+	s|%%CFLAGS%%|${CFLAGS}|g'  ${WRKSRC}/Makefile
+.if !defined(WITH_OPTIMIZED_FLAGS)
+	@${ECHO} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
+.endif
+
+do-install:
+	${MKDIR} ${DATADIR}
+	${INSTALL_PROGRAM} ${WRKSRC}/garlic       ${PREFIX}/bin
+	${INSTALL_DATA}    ${WRKSRC}/.garlicrc    ${DATADIR}
+	${INSTALL_DATA}    ${WRKSRC}/residues.pdb ${DATADIR}
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${EXAMPLESDIR}
+	@${INSTALL_DATA}    ${WRKSRC}/*.pdb        ${EXAMPLESDIR}
+	@${INSTALL_DATA}    ${WRKSRC}/*.script     ${EXAMPLESDIR}
+	@${MKDIR} ${DOCSDIR}
+	@${MKDIR} ${WRKDIR}/doc
+	@cd ${WRKDIR}/doc ; ${TAR} xvfz ${DISTDIR}/${DISTNAME}-doc${EXTRACT_SUFX}
+	@${TAR} -C ${WRKDIR}/doc/${DISTNAME} -cf - .  | \
+		${TAR} -C ${DOCSDIR} -xf -
+	@${FIND} ${DOCSDIR} | ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP}
+	@${FIND} ${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/garlic/distinfo b/biology/garlic/distinfo
new file mode 100644
index 000000000000..515690f4f9ed
--- /dev/null
+++ b/biology/garlic/distinfo
@@ -0,0 +1,2 @@
+MD5 (garlic-1.4.tar.gz) = 2cff4654d09e2049e21328f0b93fe9c2
+MD5 (garlic-1.4-doc.tar.gz) = cb418171d211cec9fc857b3e5d63803c
diff --git a/biology/garlic/files/patch-Makefile b/biology/garlic/files/patch-Makefile
new file mode 100644
index 000000000000..18a9d63d72af
--- /dev/null
+++ b/biology/garlic/files/patch-Makefile
@@ -0,0 +1,20 @@
+--- Makefile.orig	Fri May 30 20:27:25 2003
++++ Makefile	Mon Jul 28 12:01:48 2003
+@@ -1,14 +1,14 @@
+-CC = gcc
++CC = %%CC%%
+ 
+ #CCOPT = -O
+ #CCOPT = -O3
+ #CCOPT = -O3 -g3
+ #CCOPT = -ansi -pedantic -g3
+-CCOPT = -ansi -pedantic -O -Wall -Wstrict-prototypes -g3
++CCOPT = %%CFLAGS%% -I%%LOCALBASE%%/include -I%%X11BASE%%/include
+ 
+ HEADERS = defines.h typedefs.h
+ 
+-LIBPATH = -L/usr/X11R6/lib
++LIBPATH = -L%%X11BASE%%/lib
+ 
+ LINKOPT = -lX11 -lm
+ 
diff --git a/biology/garlic/pkg-descr b/biology/garlic/pkg-descr
new file mode 100644
index 000000000000..7b1a95ff6153
--- /dev/null
+++ b/biology/garlic/pkg-descr
@@ -0,0 +1,12 @@
+Free, open source molecular viewer and editor for
+protein structure, DNA structure, PDB, molecular rendering,
+biological macromolecule.
+Atoms may be drawn as spheres of different sizes.
+Bonds may be drawn as cylindrical sticks, conical sticks or as curved surfaces.
+Five types of slab are available: planar, spherical,
+semi-spherical, cylindrical and semi-cylindrical.
+The slab position and thickness are visible in a small window.
+Atomic bonds as well as atoms are treated as independent drawable objects.
+and more!
+
+WWW: http://ccp14.semo.edu/ccp/web-mirrors/garlic/garlic/
diff --git a/biology/garlic/pkg-plist b/biology/garlic/pkg-plist
new file mode 100644
index 000000000000..6bb84f75df6b
--- /dev/null
+++ b/biology/garlic/pkg-plist
@@ -0,0 +1,305 @@
+bin/garlic
+share/garlic/.garlicrc
+share/garlic/residues.pdb
+@dirrm share/garlic
+%%PORTDOCS%%share/doc/garlic/data/favicon.ico
+%%PORTDOCS%%share/doc/garlic/data/index.html
+%%PORTDOCS%%share/doc/garlic/data/garlic.gif
+%%PORTDOCS%%share/doc/garlic/favicon.ico
+%%PORTDOCS%%share/doc/garlic/refcard/favicon.ico
+%%PORTDOCS%%share/doc/garlic/refcard/index.html
+%%PORTDOCS%%share/doc/garlic/refcard/garlic.gif
+%%PORTDOCS%%share/doc/garlic/refcard/refcard.html
+%%PORTDOCS%%share/doc/garlic/techinfo/favicon.ico
+%%PORTDOCS%%share/doc/garlic/techinfo/index.html
+%%PORTDOCS%%share/doc/garlic/techinfo/garlic.gif
+%%PORTDOCS%%share/doc/garlic/mouse/favicon.ico
+%%PORTDOCS%%share/doc/garlic/mouse/neighbor.gif
+%%PORTDOCS%%share/doc/garlic/mouse/outplot.gif
+%%PORTDOCS%%share/doc/garlic/mouse/index.html
+%%PORTDOCS%%share/doc/garlic/mouse/.xvpics/outplot.gif
+%%PORTDOCS%%share/doc/garlic/mouse/.xvpics/outstr.gif
+%%PORTDOCS%%share/doc/garlic/mouse/.xvpics/outcomp.gif
+%%PORTDOCS%%share/doc/garlic/mouse/.xvpics/outrama.gif
+%%PORTDOCS%%share/doc/garlic/mouse/outstr.gif
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+%%PORTDOCS%%share/doc/garlic/mouse/outrama.gif
+%%PORTDOCS%%share/doc/garlic/mouse/garlic.gif
+%%PORTDOCS%%share/doc/garlic/README
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+%%PORTDOCS%%share/doc/garlic/download/index.html
+%%PORTDOCS%%share/doc/garlic/download/garlic.gif
+%%PORTDOCS%%share/doc/garlic/scripts/favicon.ico
+%%PORTDOCS%%share/doc/garlic/scripts/colors.script
+%%PORTDOCS%%share/doc/garlic/scripts/atoms.script
+%%PORTDOCS%%share/doc/garlic/scripts/probes.script
+%%PORTDOCS%%share/doc/garlic/scripts/bonds.script
+%%PORTDOCS%%share/doc/garlic/scripts/garlic.gif
+%%PORTDOCS%%share/doc/garlic/license/favicon.ico
+%%PORTDOCS%%share/doc/garlic/license/index.html
+%%PORTDOCS%%share/doc/garlic/license/garlic.gif
+%%PORTDOCS%%share/doc/garlic/docs.html
+%%PORTDOCS%%share/doc/garlic/index.html
+%%PORTDOCS%%share/doc/garlic/bold_statement.html
+%%PORTDOCS%%share/doc/garlic/gallery/favicon.ico
+%%PORTDOCS%%share/doc/garlic/gallery/index.html
+%%PORTDOCS%%share/doc/garlic/gallery/small1.png
+%%PORTDOCS%%share/doc/garlic/gallery/small2.png
+%%PORTDOCS%%share/doc/garlic/gallery/small3.png
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+%%PORTDOCS%%share/doc/garlic/gallery/small11.png
+%%PORTDOCS%%share/doc/garlic/gallery/small12.png
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+%%PORTDOCS%%share/doc/garlic/config/favicon.ico
+%%PORTDOCS%%share/doc/garlic/config/.garlicrc
+%%PORTDOCS%%share/doc/garlic/config/index.html
+%%PORTDOCS%%share/doc/garlic/config/garlic.gif
+%%PORTDOCS%%share/doc/garlic/support/favicon.ico
+%%PORTDOCS%%share/doc/garlic/support/index.html
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+%%PORTDOCS%%@dirrm share/doc/garlic/install
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+%%PORTDOCS%%@dirrm share/doc/garlic/features
+%%PORTDOCS%%@dirrm share/doc/garlic/download
+%%PORTDOCS%%@dirrm share/doc/garlic/data
+%%PORTDOCS%%@dirrm share/doc/garlic/cookbook
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+%%PORTDOCS%%%%EXAMPLESDIR%%/sample.script
+%%PORTDOCS%%%%EXAMPLESDIR%%/singleatom.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/singlebond.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/test.script
+%%PORTDOCS%%%%EXAMPLESDIR%%/trp.pdb
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%