From b9a65c90e7b6b358c801415762d54ab0598e576b Mon Sep 17 00:00:00 2001 From: jylefort Date: Thu, 28 Apr 2005 19:01:41 +0000 Subject: - Update to 5.0 - Cleanups PR: ports/80372 Submitted by: maintainer --- biology/nab/Makefile | 87 +-- biology/nab/distinfo | 4 +- biology/nab/files/config.h | 142 ++-- biology/nab/files/patch-Makefile | 59 +- biology/nab/files/patch-ac | 18 - biology/nab/files/patch-src:database.c | 25 - biology/nab/files/patch-src:molio.c | 10 - biology/nab/files/patch-src_Makefile | 17 + biology/nab/files/patch-src_cgen.c | 21 + biology/nab/files/patch-src_nabgrm.y | 20 + biology/nab/files/patch-tleap:database.c | 16 - biology/nab/files/patch-unitio.c | 10 - biology/nab/files/pkg-message.in | 8 + biology/nab/pkg-message | 6 - biology/nab/pkg-plist | 1190 +++++++++++++++++------------- 15 files changed, 851 insertions(+), 782 deletions(-) delete mode 100644 biology/nab/files/patch-ac delete mode 100644 biology/nab/files/patch-src:database.c delete mode 100644 biology/nab/files/patch-src:molio.c create mode 100644 biology/nab/files/patch-src_Makefile create mode 100644 biology/nab/files/patch-src_cgen.c create mode 100644 biology/nab/files/patch-src_nabgrm.y delete mode 100644 biology/nab/files/patch-tleap:database.c delete mode 100644 biology/nab/files/patch-unitio.c create mode 100644 biology/nab/files/pkg-message.in delete mode 100644 biology/nab/pkg-message (limited to 'biology/nab') diff --git a/biology/nab/Makefile b/biology/nab/Makefile index 95a223dc4cbb..0bc31fead397 100644 --- a/biology/nab/Makefile +++ b/biology/nab/Makefile @@ -6,91 +6,72 @@ # PORTNAME= nab -PORTVERSION= 4.6 +PORTVERSION= 5.0 CATEGORIES= biology -MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ \ - http://www.scripps.edu/case/ \ +MASTER_SITES= http://www.scripps.edu/case/ \ http://siegfried.utmb.edu/bdodson/ MAINTAINER= bdodson@scms.utmb.edu -COMMENT= \ - "This is nab (nucleic acid builder), a language for macromolecules" +COMMENT= A language for macromolecules BUILD_DEPENDS= ucpp:${PORTSDIR}/devel/ucpp ONLY_FOR_ARCHS= i386 -MAKE_ENV+= NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} +MAKE_ENV+= NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} \ + CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}" MAN1= nab.1 -MANCOMPRESSED= yes -USE_REINPLACE= yes +SUB_FILES= pkg-message -BINARIES= matextract matmul teLeap tss_main \ - matgen nab transform tss_next \ - matmerge nab2c tss_init +BINARIES= matextract matmul teLeap tss_main \ + matgen nab transform tss_next \ + matmerge nab2c tss_init -LIBRARIES= cifparse.a libnab.a libsym.a +LIBRARIES= cifparse.a libnab.a libsym.a -INCS= defreal.h nab.h nabcode.h nabtypes.h +INCS= defreal.h nab.h nabcode.h nabtypes.h post-extract: @${CP} ${FILESDIR}/config.h ${WRKSRC} -pre-patch: - @${REINPLACE_CMD} -e 's,,,' \ - ${WRKSRC}/cifparse/cifparse.c - post-patch: - @${RM} -f ${WRKSRC}/examples/program_7.nab.orig - @${RM} -f ${WRKSRC}/examples/program_1.c \ - ${WRKSRC}/examples/program_1.exe - @${RM} -f ${WRKSRC}/test/1ubq/a.exe - @${RM} -f ${WRKSRC}/test/1ubq/rattle_min.c - @${RM} -f ${WRKSRC}/test/1ubq/runleap.c - @${RM} -f ${WRKSRC}/test/*.exe - @${RM} -f ${WRKSRC}/tleap/utilMakeHelp.exe - @${RM} -f ${WRKSRC}/fd_data/abdna.dat.old + @${RM} -f ${WRKSRC}/examples/circle.c @${RM} -f ${WRKSRC}/reslib/conf.lib.orig - @${RM} -f ${WRKSRC}/reslib/leap/parm94.dat~ - @(cd ${WRKSRC}/reslib/leap && \ - ${FIND} . -type f -print | ${GREP} -v '\./[a-zA-Z0-9]' | \ - ${XARGS} ${RM} -f) pre-install: @cd ${WRKSRC}/src && \ - ${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall + ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} beforerealinstall do-install: - @-${MKDIR} ${PREFIX}/share/nab - @-${MKDIR} ${PREFIX}/share/nab/bin - @-${MKDIR} ${PREFIX}/share/nab/include - @-${MKDIR} ${PREFIX}/share/nab/lib + ${MKDIR} ${DATADIR}/bin ${DATADIR}/include ${DATADIR}/lib + cd ${WRKSRC}/test && ${RM} -f gbrna.pdb.lpdb rembed.out .if !defined(NOPORTDOCS) - @cd ${WRKSRC} && (${TAR} cf - examples test peptide suppose | \ - (cd ${PREFIX}/share/nab; ${TAR} xf -)) - @-${MKDIR} ${PREFIX}/share/doc/nab - ${INSTALL_MAN} ${WRKSRC}/doc/NAB.pdf ${PREFIX}/share/doc/nab + cd ${WRKSRC} && (${TAR} cf - benchmarks examples test peptide suppose | \ + (cd ${DATADIR}; ${TAR} xf -)) + ${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/doc/NAB.pdf ${DOCSDIR} .endif - @cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data | \ - (cd ${PREFIX}/share/nab; ${TAR} xf -)) - @(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}:${SHAREGRP} nab; \ - ${CHMOD} -R ugo+rX-w nab) - @-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords) - ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin + cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data leap | \ + (cd ${DATADIR}; ${TAR} xf -)) + ${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${DATADIR}/* + cd ${DATADIR} && ${LN} -sf ../NDB coords + ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin .for f in ${INCS} - ${INSTALL_DATA} ${WRKSRC}/include/${f} ${PREFIX}/include - @-(cd ${PREFIX}/share/nab/include && ${LN} -sf ${PREFIX}/include/${f} .) + ${INSTALL_DATA} ${WRKSRC}/include/${f} ${PREFIX}/include + cd ${DATADIR}/include && ${LN} -sf ${PREFIX}/include/${f} . .endfor - ${INSTALL_DATA} ${WRKSRC}/config.h ${PREFIX}/share/nab/include - ${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib - @-cd ${WRKSRC}/doc && ${GZIP_CMD} ${MAN1} - ${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz ${PREFIX}/man/man1 + ${INSTALL_DATA} ${WRKSRC}/config.h ${DATADIR} + ${INSTALL_MAN} ${WRKSRC}/doc/nab.1 ${MAN1PREFIX}/man/man1 .for f in ${BINARIES} - @cd ${PREFIX}/share/nab/bin && ${LN} -sf ../../../bin/${f} . + cd ${DATADIR}/bin && ${LN} -sf ${PREFIX}/bin/${f} . .endfor .for f in ${LIBRARIES} - @cd ${PREFIX}/share/nab/lib && ${LN} -sf ../../../lib/${f} . + ${INSTALL_DATA} ${WRKSRC}/lib/${f} ${PREFIX}/lib + cd ${DATADIR}/lib && ${LN} -sf ${PREFIX}/lib/${f} . +.endfor +.for f in blas.a lapack.a + ${INSTALL_DATA} ${WRKSRC}/lib/${f} ${DATADIR}/lib .endfor post-install: diff --git a/biology/nab/distinfo b/biology/nab/distinfo index be2704233758..186fc15e8374 100644 --- a/biology/nab/distinfo +++ b/biology/nab/distinfo @@ -1,2 +1,2 @@ -MD5 (nab-4.6.tar.gz) = ec1e51b8a9f6d5a46770b952f0e59d26 -SIZE (nab-4.6.tar.gz) = 3794078 +MD5 (nab-5.0.tar.gz) = dfcde2ddaa833f4dc24d53c87b842cf9 +SIZE (nab-5.0.tar.gz) = 5853573 diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h index cd5dece57ec8..7dd5649fc85d 100644 --- a/biology/nab/files/config.h +++ b/biology/nab/files/config.h @@ -1,114 +1,70 @@ +# NAB configuration file, created with: ./configure + ############################################################################### -# Configuration section: look at sections (1) to (4) below, making -# changes that seem necessary. For many UNIX systems, no changes -# should be necessary, but check especially the compiler options in -# section (4). -# -############################################################################### -# -# (1) You need to define the symbols NABHOME and ARCH, either on the -# make command line (e.g. "make ARCH=sun4 NABHOME=/thr/eigen/nab5") -# or as environment variables. -# -# NABHOME should be an absolute path to this directory. -# ARCH is used to distinguish compilations for various architectures. -# -# Files created by "make install" end up in: -# $NABHOME/bin/$ARCH -# $NABHOME/lib/$ARCH -# $NABHOME/include -# -# You can choose ARCH as you wish, but it would generally -# be related to the output of the "uname" command. -# + +# (1) You need to define the symbol NABHOME in your environment + +# NABHOME should be an absolute path to the top-level NAB directory; +# files are installed to the following directories: + BINDIR=$(NABHOME)/bin LIBDIR=$(NABHOME)/lib INCDIR=$(NABHOME)/include -# + ############################################################################### -# -# + + # (2) If you want to search additional libraries by default, add them # to the FLIBS variable here. (External libraries can also be linked into # NAB programs simply by including them on the command line; libraries # included in FLIBS are always searched.) -# -#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a -# -# following for linking in fortran subroutines on Sun4, Solaris 2.x -# -#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a -lF77 -lM77 -lsunmath -# -# following for HP-UX -# -#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a lapack.a blas.a -lf -lvec -# -############################################################################### -# -# (3) Set AVS to 1 if you want AVS support; if so, set AVSDIR to point to -# your AVS distribution. The directories $AVSDIR/include and $AVSDIR/lib -# must exist, and CFLAGS (below) must also be modified for AVS support. -# -AVS= 0 -# -#AVSDIR= /tsri/avs/$(ARCH)/avs -#AVSINCDIR= $(AVSDIR)/include -# -# + +FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a -lg2c + ############################################################################### -# -# (4) Modify any of the following if you need to change, e.g. to use gcc + +# (3) Modify any of the following if you need to change, e.g. to use gcc # rather than cc, etc. -# -# + SHELL= /bin/sh -# + # Set the C compiler, etc. -# -# For GNU: cc-->gcc; lex-->flex; yacc-->bison -y -t; -# Note: If you lexer is "really" flex, you need to set + +# For GNU: CC-->gcc; LEX-->flex; YACC-->bison -y -t; +# Note: If your lexer is "really" flex, you need to set # LEX=flex below. For example, on many linux distributions, # /usr/bin/lex is really just a pointer to /usr/bin/flex, # so LEX=flex is necessary. In general, gcc seems to need # flex. -# -# For 64-bit IRIX, add "-n32" unless 64-bit objects are -# needed; it is also useful to add "-Wl,-dont_warn_unused" -# to keep the loader from complaining about libraries that -# are not used. -# -# For RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR -# -#CC= -LEX= flex -YACC= yacc -AR= ar -# + +CC?= cc +CFLAGS?= +OCFLAGS=${CFLAGS} +NABFLAGS?= + +LEX= flex +YACC= yacc +AR= ar +RANLIB= ranlib + # Set the C-preprocessor. Code for a small preprocessor is in -# uccp-0.7; it gets installed as $(NABHOME)/bin/$(ARCH)/ucpp; +# uccp-1.3; it gets installed as $(NABHOME)/bin/ucpp; # this should generally *not* be changed. -# Changed 14 Feb 2003 to use the ucpp port (FreeBSD). MLD -# -# For FreeBSD 4.x, I had problems using the system C-preprocessor. MLD -# + CPP= ucpp -l -# -# Use these CFLAGS if AVS = 0 -# -# Pick up initial CFLAGS from /etc/make.conf instead of here -# This is a Berkeley make- (pmake-)specific construct -CFLAGS+= -OCFLAGS= ${CFLAGS} -NABFLAGS= -# -# Use these CFLAGS if AVS = 1 -# -#CFLAGS= -g -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR) -#OCFLAGS= -O -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR) -# -# -# For Win95/98, set SFX to ".exe"; for Unix,NT leave it empty: -# -#SFX=.exe + +# If you are going to use the Fortran lapack and blas libraries, you need +# to set the compiler information here. (Also, add the appropriate entries +# to the FLIBS variable, above.) + +FC?=f77 +FFLAGS?= +FOPTFLAGS=${FFLAGS} +FREEFORMAT_FLAG=-ffree-form +LAPACK=install +BLAS=install + +# For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty: + SFX= -# + diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile index 493b85bcda86..d754d329ca56 100644 --- a/biology/nab/files/patch-Makefile +++ b/biology/nab/files/patch-Makefile @@ -1,28 +1,30 @@ ---- Makefile.orig Tue May 18 15:46:55 2004 -+++ Makefile Thu Jul 1 09:03:32 2004 -@@ -1,16 +1,15 @@ - # top-level Makefile for the NAB suite of programs +--- Makefile.orig Thu Apr 7 20:18:20 2005 ++++ Makefile Mon Apr 25 13:37:39 2005 +@@ -2,42 +2,39 @@ -+all: compiler test - compiler: - -mkdir bin lib include + include config.h + ++all: install test ++ + install: + -mkdir $(BINDIR) $(LIBDIR) $(INCDIR) - (cd ucpp-1.3; make install ) - (cd byacc; make install ) - (cd cifparse; make install ) - (cd src; make install ) - (cd nss; make install ) - (cd tleap; make install ) -- @echo -- @echo "completed installation of NAB version 4" -- @echo -+# @echo -+# @echo "completed installation of NAB version 4" -+# @echo - - # note: "make test" needs to follow "make", since it is very hard to - # tell if the compiler is completely "made" or not. -@@ -19,18 +18,15 @@ - (cd nss; make test ) +- (cd lapack; make $(LAPACK) ) +- (cd blas; make $(BLAS) ) +- (cd cifparse; make install ) +- (cd src; make install ) +- (cd nss; make install ) +- (cd tleap; make install ) ++ (cd lapack; env NABHOME=.. make $(LAPACK) ) ++ (cd blas; env NABHOME=.. make $(BLAS) ) ++ (cd cifparse; env NABHOME=.. make install ) ++ (cd src; env NABHOME=.. make install ) ++ (cd nss; env NABHOME=.. make install ) ++ (cd tleap; env NABHOME=.. make install ) + @echo + @echo "completed installation of NAB version 5" + @echo clean: - (cd ucpp-1.3; make clean ) @@ -31,14 +33,25 @@ (cd src; make clean ) (cd nss; make clean ) (cd tleap; make clean ) + (cd lapack; make clean ) + (cd blas; make clean ) - + - uninstall: + uninstall: clean - (cd ucpp-1.3; make uninstall ) (cd cifparse; make uninstall ) (cd src; make uninstall ) (cd nss; make uninstall ) (cd tleap; make uninstall ) -/bin/rm config.h + -rm -rf $(BINDIR) $(LIBDIR) $(INCDIR) - + + # note: "make test" needs to follow "make", since it is very hard to + # tell if the compiler is completely "made" or not. + + test:: +- (cd test; make test) +- (cd nss; make test) ++ (cd test; env NABHOME=.. make test) ++ (cd nss; env NABHOME=.. make test) diff --git a/biology/nab/files/patch-ac b/biology/nab/files/patch-ac deleted file mode 100644 index e3c6e85535de..000000000000 --- a/biology/nab/files/patch-ac +++ /dev/null @@ -1,18 +0,0 @@ -*** src/Makefile.orig Mon Nov 13 13:37:07 2000 ---- src/Makefile Mon Jan 29 12:33:37 2001 -*************** -*** 175,180 **** ---- 175,187 ---- - cp defreal.h $(INCDIR) - cp nab.h $(INCDIR) - -+ beforerealinstall: -+ $(CC) -DBINDIR='"$(PREFIX)/bin"' \ -+ -DINCDIR='"$(PREFIX)/include"' \ -+ -DLIBDIR='"$(PREFIX)/lib"' \ -+ $(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' -DFLIBS='"$(FLIBS)"' \ -+ -o ../bin/nab nab.c -+ - uninstall: clean - -rm -f \ - $(BINDIR)/nab2c$(SFX) $(BINDIR)/nab$(SFX) $(INCDIR)/nabcode.h \ diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c deleted file mode 100644 index 14e70c31326a..000000000000 --- a/biology/nab/files/patch-src:database.c +++ /dev/null @@ -1,25 +0,0 @@ ---- src/database.c.orig Thu Nov 16 15:37:11 2000 -+++ src/database.c Fri Feb 14 12:15:53 2003 -@@ -64,6 +64,13 @@ - * The TOTAL database name MUST NEVER be longer than - * can be contained in the String object. - */ -+#if (defined(__unix__) || defined(unix)) && !defined(USG) -+#include -+#endif -+ -+#if defined(BSD) -+#include -+#endif - - - -@@ -71,7 +78,7 @@ - - #include - #include --#include -+#include - - #include "database.h" - diff --git a/biology/nab/files/patch-src:molio.c b/biology/nab/files/patch-src:molio.c deleted file mode 100644 index 656042bb2f24..000000000000 --- a/biology/nab/files/patch-src:molio.c +++ /dev/null @@ -1,10 +0,0 @@ ---- src/molio.c.orig Mon May 10 16:53:34 2004 -+++ src/molio.c Fri Jun 18 23:26:01 2004 -@@ -1,7 +1,6 @@ - #include - #include - #include --#include - #include - #include - #include diff --git a/biology/nab/files/patch-src_Makefile b/biology/nab/files/patch-src_Makefile new file mode 100644 index 000000000000..23bce990b0e3 --- /dev/null +++ b/biology/nab/files/patch-src_Makefile @@ -0,0 +1,17 @@ +--- src/Makefile.orig Thu Apr 7 20:17:27 2005 ++++ src/Makefile Tue Apr 26 12:54:15 2005 +@@ -181,6 +181,14 @@ + cp defreal.h $(INCDIR) + cp nab.h $(INCDIR) + ++beforerealinstall: ++ $(CC) -DBINDIR='"$(PREFIX)/bin"' \ ++ -DINCDIR='"$(PREFIX)/include"' \ ++ -DLIBDIR='"$(NABHOME)/lib"' \ ++ $(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' \ ++ -DFLIBS='"$(PREFIX)/share/nab/lib/libsym.a $(PREFIX)/share/nab/lib/lapack.a $(PREFIX)/share/nab/lib/blas.a -lg2c"' \ ++ -static -o ../bin/nab${SFX} nab.c ++ + uninstall: clean + -rm -f \ + $(BINDIR)/nab2c$(SFX) $(BINDIR)/nab$(SFX) $(INCDIR)/nabcode.h \ diff --git a/biology/nab/files/patch-src_cgen.c b/biology/nab/files/patch-src_cgen.c new file mode 100644 index 000000000000..c6538200406e --- /dev/null +++ b/biology/nab/files/patch-src_cgen.c @@ -0,0 +1,21 @@ +--- src/cgen.c.orig Thu Apr 7 20:17:27 2005 ++++ src/cgen.c Sun Apr 17 20:21:22 2005 +@@ -102,6 +102,7 @@ + void CG_genpids( NODE_T * ); + void CG_genpdecl( NODE_T * ); + char *CG_gentemp( int ); ++void CG_gennull( void ); + + static int getdims( NODE_T *, int, int, int *, NODE_T *[] ); + static NODE_T *mk_arraysize( int, NODE_T *[], int ); +@@ -115,6 +116,10 @@ + static void CG_debug( char [], NODE_T *, int ); + + FILE *tmpfile(); ++ ++void CG_gennull( ) ++{ ++} + + int CG_init( char cfname[], int aopt ) + { diff --git a/biology/nab/files/patch-src_nabgrm.y b/biology/nab/files/patch-src_nabgrm.y new file mode 100644 index 000000000000..348e3a157d8b --- /dev/null +++ b/biology/nab/files/patch-src_nabgrm.y @@ -0,0 +1,20 @@ +--- src/nabgrm.y.orig Thu Apr 7 20:17:27 2005 ++++ src/nabgrm.y Sun Apr 17 20:21:36 2005 +@@ -41,6 +41,8 @@ + + # define YYSTYPE_IS_DECLARED 1 + ++#define YYSTYPE_IS_DECLARED 1 ++ + %} + + %token SYM_ADDRESS +@@ -299,7 +301,7 @@ + f_stmtpart SYM_RBRACE + { CG_genestmts( TRUE ); + CG_genop( NULL, SYM_RBRACE ); } +- SYM_SEMICOLON ; ++ SYM_SEMICOLON { CG_gennull ( ); } ; + f_defpart : lv_decls + | { $$ = NULL; } ; + lv_decls : var_decl diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c deleted file mode 100644 index c6004d1d9a24..000000000000 --- a/biology/nab/files/patch-tleap:database.c +++ /dev/null @@ -1,16 +0,0 @@ ---- tleap/database.c.orig Sat Nov 9 18:36:58 2002 -+++ tleap/database.c Wed Jan 29 09:56:46 2003 -@@ -185,6 +185,13 @@ - } - - -+#if (defined(__unix__) || defined(unix)) && !defined(USG) -+#include -+#endif -+ -+#if defined(BSD) -+#include -+#endif - - - diff --git a/biology/nab/files/patch-unitio.c b/biology/nab/files/patch-unitio.c deleted file mode 100644 index 8b3048548a01..000000000000 --- a/biology/nab/files/patch-unitio.c +++ /dev/null @@ -1,10 +0,0 @@ ---- tleap/unitio.c.orig Sat Nov 9 18:37:02 2002 -+++ tleap/unitio.c Fri Feb 14 12:20:38 2003 -@@ -5958,6 +5958,7 @@ - *TODO: Add CAP information - */ - #define AMBERINDEX(i) 3*(i-1) -+#undef INTFORMAT - #define INTFORMAT "%6d" - #define DBLFORMAT "%16.8lE" - #define LBLFORMAT "%-4s" diff --git a/biology/nab/files/pkg-message.in b/biology/nab/files/pkg-message.in new file mode 100644 index 000000000000..e89f4516b02e --- /dev/null +++ b/biology/nab/files/pkg-message.in @@ -0,0 +1,8 @@ +------------------------------------------------------------------------------- +You must set the environment variable NABHOME to + + %%DATADIR%% + +before nab is used. This is needed so that nab can find its residue and +structure databases. +------------------------------------------------------------------------------- diff --git a/biology/nab/pkg-message b/biology/nab/pkg-message deleted file mode 100644 index 349abd45952d..000000000000 --- a/biology/nab/pkg-message +++ /dev/null @@ -1,6 +0,0 @@ -------------------------------------------------------------------------------- -You must set the environment variable NABHOME before nab is used. This is -needed so that nab can find its residue and structure databases. This should be -NABHOME=${PREFIX}/share/nab, where ${PREFIX} was the value of the PREFIX -makefile variable when nab was built. -------------------------------------------------------------------------------- diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist index 191041c7cab2..7e3d1c88e4e5 100644 --- a/biology/nab/pkg-plist +++ b/biology/nab/pkg-plist @@ -16,529 +16,667 @@ include/nabtypes.h lib/cifparse.a lib/libnab.a lib/libsym.a -%%DOCSDIR%%/NAB.pdf -share/nab/bin/matextract -share/nab/bin/matgen -share/nab/bin/matmerge -share/nab/bin/matmul -share/nab/bin/nab -share/nab/bin/nab2c -share/nab/bin/teLeap -share/nab/bin/transform -share/nab/bin/tss_init -share/nab/bin/tss_main -share/nab/bin/tss_next -share/nab/coords -share/nab/dgdb/adna.basepair.db -share/nab/dgdb/adna.nucleotide.db -share/nab/dgdb/adna.stack.db -share/nab/dgdb/arna.basepair.db -share/nab/dgdb/arna.nucleotide.db -share/nab/dgdb/arna.stack.db -share/nab/dgdb/bdna.basepair.db -share/nab/dgdb/bdna.nucleotide.db -share/nab/dgdb/bdna.stack.db -share/nab/dgdb/dna.basepair.db -share/nab/dgdb/rna.basepair.db -share/nab/dgdb/trna.basepair.db -share/nab/dgdb/trna.nucleotide.db -share/nab/dgdb/trna.stack.db -share/nab/dgdb/zdna.basepair.db -share/nab/dgdb/zdna.nucleotide.db -share/nab/dgdb/zdna.stack.db -share/nab/dgdb/basepairs/aa.I.pdb -share/nab/dgdb/basepairs/aa.II.pdb -share/nab/dgdb/basepairs/aa.V.pdb -share/nab/dgdb/basepairs/aa.Va.pdb -share/nab/dgdb/basepairs/ac.XXV.pdb -share/nab/dgdb/basepairs/ac.XXVI.pdb -share/nab/dgdb/basepairs/ag.IX.pdb -share/nab/dgdb/basepairs/ag.VIII.pdb -share/nab/dgdb/basepairs/ag.X.pdb -share/nab/dgdb/basepairs/ag.XI.pdb -share/nab/dgdb/basepairs/at.XX.pdb -share/nab/dgdb/basepairs/at.XXI.pdb -share/nab/dgdb/basepairs/at.XXIII.pdb -share/nab/dgdb/basepairs/at.XXIV.pdb -share/nab/dgdb/basepairs/au.XX.pdb -share/nab/dgdb/basepairs/au.XXI.pdb -share/nab/dgdb/basepairs/au.XXIII.pdb -share/nab/dgdb/basepairs/au.XXIV.pdb 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%%DATADIR%%/reslib/rna.amberua +@dirrm %%DATADIR%%/reslib/rna.amber94 +@dirrm %%DATADIR%%/reslib/protein.opls +@dirrm %%DATADIR%%/reslib/protein.amber94 +@dirrm %%DATADIR%%/reslib/pro-dna.nmr +@dirrm %%DATADIR%%/reslib/hetatm.amber94 +@dirrm %%DATADIR%%/reslib/dna3 +@dirrm %%DATADIR%%/reslib/dna.amberua +@dirrm %%DATADIR%%/reslib/dna.amber94 +@dirrm %%DATADIR%%/reslib/bdna.std +@dirrm %%DATADIR%%/reslib/axes +@dirrm %%DATADIR%%/reslib/arna.std +@dirrm %%DATADIR%%/reslib/adna.std +@dirrm %%DATADIR%%/reslib +@dirrm %%DATADIR%%/lib +@dirrm %%DATADIR%%/leap/prep +@dirrm %%DATADIR%%/leap/parm +@dirrm %%DATADIR%%/leap/lib +@dirrm %%DATADIR%%/leap/cmd +@dirrm %%DATADIR%%/leap +@dirrm %%DATADIR%%/include +@dirrm %%DATADIR%%/fd_data +@dirrm %%DATADIR%%/dgdb/stacking +@dirrm %%DATADIR%%/dgdb/basepairs +@dirrm %%DATADIR%%/dgdb +@dirrm %%DATADIR%%/bin +%%PORTDOCS%%@dirrm %%DATADIR%%/benchmarks +%%PORTDOCS%%@dirrm %%DATADIR%%/examples +%%PORTDOCS%%@dirrm %%DATADIR%%/peptide +%%PORTDOCS%%@dirrm %%DATADIR%%/suppose +%%PORTDOCS%%@dirrm %%DATADIR%%/test +@dirrm %%DATADIR%% +%%PORTDOCS%%@dirrm %%DOCSDIR%% -- cgit