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This commit is contained in:
Lionel Sambuc
2013-09-26 17:14:40 +02:00
commit 785076ae39
74991 changed files with 4380255 additions and 0 deletions
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41
biology/Makefile Normal file
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# $NetBSD: Makefile,v 1.36 2013/03/16 12:45:33 asau Exp $
#
COMMENT= Software for the biological sciences
SUBDIR+= arka
SUBDIR+= azara
SUBDIR+= bioperl
SUBDIR+= bodr
SUBDIR+= chemical-mime-data
SUBDIR+= chemtool
SUBDIR+= clustalw
SUBDIR+= coalesce
SUBDIR+= fastDNAml
SUBDIR+= fluctuate
SUBDIR+= genesplicer
SUBDIR+= glimmer
SUBDIR+= gnome-chemistry-utils
SUBDIR+= gp
SUBDIR+= gromacs
SUBDIR+= hmmer
SUBDIR+= lucy
SUBDIR+= mopac
SUBDIR+= mpqc
SUBDIR+= mummer
SUBDIR+= nut
SUBDIR+= openbabel
SUBDIR+= pdbalign
SUBDIR+= phylip
SUBDIR+= plink
SUBDIR+= plinkseq
SUBDIR+= primer3
SUBDIR+= profit
SUBDIR+= puzzle
SUBDIR+= py-mol
SUBDIR+= rasmol
SUBDIR+= sewer
SUBDIR+= stride
SUBDIR+= xylem
.include "../mk/misc/category.mk"

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biology/arka/DESCR Normal file
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Arka is a program that serves as a graphical interface for the programs from
the GP package.
Furthermore, it has some interesting functions of it's own. The main scope
of the program is the manipulation and visualisation of DNA / RNA / protein
sequences.

39
biology/arka/Makefile Normal file
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# $NetBSD: Makefile,v 1.13 2012/09/11 20:32:10 asau Exp $
#
DISTNAME= arka-0.11
PKGREVISION= 2
CATEGORIES= biology
MASTER_SITES= http://www.bioinformatics.org/genpak/download/
EXTRACT_SUFX= .tgz
MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://www.bioinformatics.org/genpak/
COMMENT= Graphic interface for the programs from the GP package
DEPENDS+= gp-[0-9]*:../../biology/gp
CONF_FILES= ${PREFIX}/share/examples/arka/arkarc ${PKG_SYSCONFDIR}/arkarc
CPPFLAGS+= -DARKA_GLOBAL=\"${PKG_SYSCONFDIR}/arkarc\"
CPPFLAGS+= -DARKA_PROGRAMS=\"${PKG_SYSCONFDIR}/arkarc\"
INSTALLATION_DIRS= bin ${PKGMANDIR}/man1 share/pixmaps share/doc/arka \
share/examples/arka
USE_TOOLS+= gunzip
post-build:
cd ${WRKSRC} && ${GUNZIP_CMD} arka.1.gz
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/arka ${DESTDIR}${PREFIX}/bin
${INSTALL_MAN} ${WRKSRC}/arka.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
.for f in arka_16x16.xpm arka_32x32.xpm
${INSTALL_DATA} ${WRKSRC}/icons/${f} ${DESTDIR}${PREFIX}/share/pixmaps
.endfor
.for f in CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT TODO.TXT
${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/doc/arka
.endfor
${INSTALL_DATA} ${WRKSRC}/arkarc ${DESTDIR}${PREFIX}/share/examples/arka
.include "../../x11/gtk/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

11
biology/arka/PLIST Normal file
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@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
bin/arka
man/man1/arka.1
share/doc/arka/CHANGES.TXT
share/doc/arka/INSTALL.TXT
share/doc/arka/LICENSE.TXT
share/doc/arka/README.TXT
share/doc/arka/TODO.TXT
share/examples/arka/arkarc
share/pixmaps/arka_16x16.xpm
share/pixmaps/arka_32x32.xpm

7
biology/arka/distinfo Normal file
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$NetBSD: distinfo,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
SHA1 (arka-0.11.tgz) = 7b1e373cb7e74a70da8c2c423dd6d7f3fecd6960
RMD160 (arka-0.11.tgz) = 203d155b292cd34cd00f36b4162756081f03a6fc
Size (arka-0.11.tgz) = 280123 bytes
SHA1 (patch-aa) = 97321d794aa8dbe525ac50eb8f2409572485aa56
SHA1 (patch-ab) = 935e3100a86cc6b43ff62a202f6337765a003c6a

20
biology/arka/patches/patch-aa Normal file
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$NetBSD: patch-aa,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
--- src/Makefile.orig 2001-05-09 22:28:41.000000000 +0200
+++ src/Makefile
@@ -1,5 +1,5 @@
CC=gcc
-CFLAGS=`gtk-config --cflags` -Wall
+CFLAGS+=$(CPPFLAGS) `gtk-config --cflags`
objects = komunikat.o main.o file.o interface.o genpak.o rcfile.o \
graph.o graph3d.o help.o programs.o options.o misc.o seqed.o search.o \
@@ -10,7 +10,7 @@ all: arka
mv arka ..
arka: $(objects)
- gcc -o arka $(objects) `gtk-config --libs` -lm
+ gcc $(LDFLAGS) -o arka $(objects) `gtk-config --libs` -lm
$(objects): main.h

13
biology/arka/patches/patch-ab Normal file
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@@ -0,0 +1,13 @@
$NetBSD: patch-ab,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
--- src/options.c.orig 2001-05-04 15:36:12.000000000 +0200
+++ src/options.c
@@ -50,7 +50,7 @@ int options_initialize(opt_s *opt) {
opt->command_history_size = 20 ;
opt->file_history_size = 5 ;
- opt->wdir = my_strdup(getenv("PWD")) ;
+ opt->wdir = getcwd(NULL, 0);
opt->wdir = realloc(opt->wdir, strlen(opt->wdir) + 2000) ;
strcat(opt->wdir, "/") ;

1
biology/azara/DESCR Normal file
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Azara is a suite of programs to process and view NMR data.

37
biology/azara/Makefile Normal file
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# $NetBSD: Makefile,v 1.13 2013/01/19 20:23:34 riastradh Exp $
#
DISTNAME= azara-2.7-src
PKGNAME= azara-2.7
PKGREVISION= 5
CATEGORIES= biology
MASTER_SITES= http://www.ccpn.ac.uk/download/azara/
MAINTAINER= mchittur@cs.nmsu.edu
HOMEPAGE= http://www.ccpn.ac.uk/azara/
COMMENT= Programs to process and view NMR data
CONFLICTS= connect-[0-9]*
MAKE_JOBS_SAFE= no
WRKSRC= ${WRKDIR}/azara-2.7
MAKE_FILE= makefile
INSTALLATION_DIRS= bin
PROGFILES= azara bin2asc combine connect contours deflate \
extract float2int int2float look_at look_byte look_for mat2par \
par2mat peak_find peak_fit plot1 plot2 process project reflate \
slides swap unblock viewer
do-install:
set -e; cd ${WRKSRC}/bin; \
${INSTALL_PROGRAM} ${PROGFILES} ${DESTDIR}${PREFIX}/bin
.include "../../graphics/glu/buildlink3.mk"
.include "../../graphics/glut/buildlink3.mk"
.include "../../x11/libX11/buildlink3.mk"
.include "../../x11/libXpm/buildlink3.mk"
.include "../../mk/motif.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

26
biology/azara/PLIST Normal file
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@comment $NetBSD: PLIST,v 1.1.1.1 2005/11/05 01:47:41 minskim Exp $
bin/azara
bin/bin2asc
bin/combine
bin/connect
bin/contours
bin/deflate
bin/extract
bin/float2int
bin/int2float
bin/look_at
bin/look_byte
bin/look_for
bin/mat2par
bin/par2mat
bin/peak_find
bin/peak_fit
bin/plot1
bin/plot2
bin/process
bin/project
bin/reflate
bin/slides
bin/swap
bin/unblock
bin/viewer

10
biology/azara/distinfo Normal file
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@@ -0,0 +1,10 @@
$NetBSD: distinfo,v 1.3 2006/01/04 21:57:08 joerg Exp $
SHA1 (azara-2.7-src.tar.gz) = 53caa85953f700cdc4ec9ef26d2bb7d9448b77b0
RMD160 (azara-2.7-src.tar.gz) = 2426102dbb87984f88ec1266b72d2e307484af0c
Size (azara-2.7-src.tar.gz) = 565272 bytes
SHA1 (patch-aa) = 1066c1e1b070020bbdd18439b27e15d359dd5e69
SHA1 (patch-ab) = 46e512fba5b00cb36cd2b2d50db4919875124309
SHA1 (patch-ac) = 12b37403ce7107989d2e0e5c7e9b3b6868464f5c
SHA1 (patch-ad) = 0da330b12768124586f786c7e980d540a4414d54
SHA1 (patch-ae) = d87b2cdcc33a423eba3a17a95cc66d8c13390e81

31
biology/azara/patches/patch-aa Normal file
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@@ -0,0 +1,31 @@
$NetBSD: patch-aa,v 1.1.1.1 2005/11/05 01:47:41 minskim Exp $
--- ENVIRONMENT.orig 2002-11-01 07:10:11.000000000 -0700
+++ ENVIRONMENT
@@ -40,14 +40,14 @@ XPM_FLAG = -DUSE_XPM
XPM_LIB = -lXpm
# X11 libraries
-X11_LIB = -lX11 -lPW
+#X11_LIB = -lX11 -lPW
# non-SGI platforms do not need PW
-#X11_LIB = -lX11
+X11_LIB = -lX11
# below uses shared libraries
#X11_LIB = -lX11_s -lPW
# Motif libraries
-MOTIF_LIB = -lXm -lXt
+MOTIF_LIB = -L${X11BASE}/lib -Wl,-R${X11BASE}/lib -L${PREFIX}/lib -Wl,-R${PREFIX}/lib -lXm -lXt
# below uses shared libraries
#MOTIF_LIB = -lXm_s -lXt_s
@@ -58,7 +58,7 @@ MOTIF_LIB = -lXm -lXt
#GL_LIB_DIR = $(X11_LIB_DIR) -I/usr/local/mesa/lib
# GL libraries
-GL_LIB = -lglut -lGLU -lGL -lXmu -lX11 -lXext
+GL_LIB = -L${X11BASE}/lib -Wl,-R${X11BASE}/lib -L${PREFIX}/lib -Wl,-R${PREFIX}/lib -lglut -lGLU -lGL -lXmu -lXi -lX11 -lXext
# set up ENDIAN_FLAG as required
# WRITE_ENDIAN_PAR if want endianess written to par file

197
biology/azara/patches/patch-ab Normal file
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@@ -0,0 +1,197 @@
$NetBSD: patch-ab,v 1.1.1.1 2005/11/05 01:47:41 minskim Exp $
--- help/makefile.orig 2002-11-01 05:27:27.000000000 -0700
+++ help/makefile
@@ -37,97 +37,97 @@ globals:
.c.o:; $(CC) -c $(CFLAGS) $<
hlp:
- txt2hlp azara
- txt2hlp combine
- txt2hlp components
- txt2hlp connect
- txt2hlp contours
- txt2hlp deflate
- txt2hlp extract
- txt2hlp peak_find
- txt2hlp peak_fit
- txt2hlp plot1
- txt2hlp plot2
- txt2hlp process
- txt2hlp project
- txt2hlp slides
- txt2hlp reflate
- txt2hlp unblock
- txt2hlp viewer
- txt2hlp plot2/baseline
- txt2hlp plot2/data
- txt2hlp plot2/extract
- txt2hlp plot2/levels
- txt2hlp plot2/object
- txt2hlp plot2/output
- txt2hlp plot2/peak
- txt2hlp plot2/peaks
- txt2hlp plot2/phase
- txt2hlp plot2/property
- txt2hlp plot2/region
- txt2hlp plot2/rowcol
- txt2hlp plot2/save
- txt2hlp plot2/tracking
- txt2hlp plot1/button
- txt2hlp plot1/data
- txt2hlp plot1/object
- txt2hlp plot1/output
- txt2hlp plot1/property
- txt2hlp plot1/region
- txt2hlp plot1/slider
- txt2hlp plot1/text
+ ./txt2hlp azara
+ ./txt2hlp combine
+ ./txt2hlp components
+ ./txt2hlp connect
+ ./txt2hlp contours
+ ./txt2hlp deflate
+ ./txt2hlp extract
+ ./txt2hlp peak_find
+ ./txt2hlp peak_fit
+ ./txt2hlp plot1
+ ./txt2hlp plot2
+ ./txt2hlp process
+ ./txt2hlp project
+ ./txt2hlp slides
+ ./txt2hlp reflate
+ ./txt2hlp unblock
+ ./txt2hlp viewer
+ ./txt2hlp plot2/baseline
+ ./txt2hlp plot2/data
+ ./txt2hlp plot2/extract
+ ./txt2hlp plot2/levels
+ ./txt2hlp plot2/object
+ ./txt2hlp plot2/output
+ ./txt2hlp plot2/peak
+ ./txt2hlp plot2/peaks
+ ./txt2hlp plot2/phase
+ ./txt2hlp plot2/property
+ ./txt2hlp plot2/region
+ ./txt2hlp plot2/rowcol
+ ./txt2hlp plot2/save
+ ./txt2hlp plot2/tracking
+ ./txt2hlp plot1/button
+ ./txt2hlp plot1/data
+ ./txt2hlp plot1/object
+ ./txt2hlp plot1/output
+ ./txt2hlp plot1/property
+ ./txt2hlp plot1/region
+ ./txt2hlp plot1/slider
+ ./txt2hlp plot1/text
html:
- txt2html azara
- txt2html combine
- txt2html components
- txt2html connect
- txt2html contours
- txt2html deflate
- txt2html extract
- txt2html peak_find
- txt2html peak_fit
- txt2html plot1
- txt2html plot2
- txt2html process
- txt2html project
- txt2html slides
- txt2html reflate
- txt2html unblock
- txt2html viewer
- txt2html plot2/baseline
- txt2html plot2/data
- txt2html plot2/extract
- txt2html plot2/levels
- txt2html plot2/object
- txt2html plot2/output
- txt2html plot2/peak
- txt2html plot2/peaks
- txt2html plot2/phase
- txt2html plot2/property
- txt2html plot2/region
- txt2html plot2/rowcol
- txt2html plot2/save
- txt2html plot2/tracking
- txt2html plot1/button
- txt2html plot1/data
- txt2html plot1/object
- txt2html plot1/output
- txt2html plot1/property
- txt2html plot1/region
- txt2html plot1/slider
- txt2html plot1/text
- txt2html CHANGES
- txt2html INSTALL
- txt2html README-2.7
- txt2html CHANGES-1.0-1
- txt2html CHANGES-1.0-2
- txt2html CHANGES-1.0-3
- txt2html CHANGES-2.0-0
- txt2html CHANGES-2.5-0
- txt2html CHANGES-2.6-0
- txt2html CHANGES-2.7-0
- txt2html LICENSE
+ ./txt2html azara
+ ./txt2html combine
+ ./txt2html components
+ ./txt2html connect
+ ./txt2html contours
+ ./txt2html deflate
+ ./txt2html extract
+ ./txt2html peak_find
+ ./txt2html peak_fit
+ ./txt2html plot1
+ ./txt2html plot2
+ ./txt2html process
+ ./txt2html project
+ ./txt2html slides
+ ./txt2html reflate
+ ./txt2html unblock
+ ./txt2html viewer
+ ./txt2html plot2/baseline
+ ./txt2html plot2/data
+ ./txt2html plot2/extract
+ ./txt2html plot2/levels
+ ./txt2html plot2/object
+ ./txt2html plot2/output
+ ./txt2html plot2/peak
+ ./txt2html plot2/peaks
+ ./txt2html plot2/phase
+ ./txt2html plot2/property
+ ./txt2html plot2/region
+ ./txt2html plot2/rowcol
+ ./txt2html plot2/save
+ ./txt2html plot2/tracking
+ ./txt2html plot1/button
+ ./txt2html plot1/data
+ ./txt2html plot1/object
+ ./txt2html plot1/output
+ ./txt2html plot1/property
+ ./txt2html plot1/region
+ ./txt2html plot1/slider
+ ./txt2html plot1/text
+ ./txt2html CHANGES
+ ./txt2html INSTALL
+ ./txt2html README-2.7
+ ./txt2html CHANGES-1.0-1
+ ./txt2html CHANGES-1.0-2
+ ./txt2html CHANGES-1.0-3
+ ./txt2html CHANGES-2.0-0
+ ./txt2html CHANGES-2.5-0
+ ./txt2html CHANGES-2.6-0
+ ./txt2html CHANGES-2.7-0
+ ./txt2html LICENSE
clean:
rm *.o
@@ -135,4 +135,4 @@ clean:
realclean:
rm *.o
rm txt2hlp
- rm txt2html
+ rM Txt2html

12
biology/azara/patches/patch-ac Normal file
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@@ -0,0 +1,12 @@
$NetBSD: patch-ac,v 1.1 2005/11/19 17:23:47 kristerw Exp $
--- global/macros.h.orig 2005-11-19 18:14:27.000000000 +0100
+++ global/macros.h 2005-11-19 18:14:34.000000000 +0100
@@ -2,7 +2,6 @@
#define _incl_macros
#include <stdio.h>
-#include <malloc.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>

19
biology/azara/patches/patch-ad Normal file
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@@ -0,0 +1,19 @@
$NetBSD: patch-ad,v 1.1 2006/01/04 21:57:08 joerg Exp $
--- help/txt2hlp.c.orig 2006-01-04 21:49:13.000000000 +0000
+++ help/txt2hlp.c
@@ -26,7 +26,7 @@ static void print_line(String line, FILE
}
}
-void main(int argc, char **argv)
+int main(int argc, char **argv)
{
int i, count;
char *prefix, *ptr, *full_prefix;
@@ -129,4 +129,5 @@ void main(int argc, char **argv)
fclose(fp_in);
fclose(fp_out);
+ return(0);
}

20
biology/azara/patches/patch-ae Normal file
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@@ -0,0 +1,20 @@
$NetBSD: patch-ae,v 1.1 2006/01/04 21:57:09 joerg Exp $
--- help/txt2html.c.orig 2006-01-04 21:51:17.000000000 +0000
+++ help/txt2html.c
@@ -190,7 +190,7 @@ static void print_line(String line, FILE
fprintf(fp, "\n");
}
-void main(int argc, char **argv)
+int main(int argc, char **argv)
{
char *prefix, *name, *ptr;
Line input_file, output_file, line, module, error_msg;
@@ -248,4 +248,6 @@ void main(int argc, char **argv)
fclose(fp_in);
fclose(fp_out);
+
+ return(0);
}

11
biology/bioperl/DESCR Normal file
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@@ -0,0 +1,11 @@
The Bioperl project is a coordinated effort to collect computational
methods routinely used in bioinformatics into a set of standard
CPAN-style, well-documented, and freely available Perl modules. Perl
provides unparalleled support for many tasks common in bioinformatics
yet there are no standard Perl modules for biology. Bioperl hopes to
help fill this void.
Bioperl modules and source code will always be freely available
under the same terms as Perl itself. The Bioperl project is open to
all and we invite suggestions and participation from the larger
bioinformatics community.

33
biology/bioperl/Makefile Normal file
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@@ -0,0 +1,33 @@
# $NetBSD: Makefile,v 1.24 2013/05/31 12:39:38 wiz Exp $
#
DISTNAME= bioperl-0.7.0
PKGREVISION= 7
CATEGORIES= biology
MASTER_SITES= http://bioperl.org/DIST/old_releases/
MAINTAINER= pkgsrc-users@NetBSD.org
HOMEPAGE= http://bioperl.org/
COMMENT= Perl tools for computational molecular biology
USE_TOOLS+= pax
REPLACE_PERL+= Bio/LiveSeq/Chain.pm
REPLACE_PERL+= Bio/SeqIO/game/featureHandler.pm
REPLACE_PERL+= Bio/Tools/Blast/Run/postclient.pl
REPLACE_PERL+= examples/gsequence
REPLACE_PERL+= examples/*.pl
REPLACE_PERL+= examples/blast/*.pl
REPLACE_PERL+= examples/root_object/*.pl
REPLACE_PERL+= examples/root_object/vector/vector.pl
REPLACE_PERL+= examples/seq/*.pl
PERL5_PACKLIST= auto/Bio/.packlist
INSTALLATION_DIRS= share/examples/bioperl
post-install:
cd ${WRKSRC}/examples && pax -rw . ${DESTDIR}${PREFIX}/share/examples/bioperl
.include "../../lang/perl5/module.mk"
.include "../../mk/bsd.pkg.mk"

74
biology/bioperl/PLIST Normal file
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@@ -0,0 +1,74 @@
@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
share/examples/bioperl/blast/out/blastn.2.gz
share/examples/bioperl/blast/out/blastn.2.wu.gz
share/examples/bioperl/blast/out/blastp.1.gcg.gz
share/examples/bioperl/blast/out/blastp.1.gz
share/examples/bioperl/blast/out/blastp.2.gz
share/examples/bioperl/blast/out/blastp.2.nogap.gz
share/examples/bioperl/blast/out/blastp.2.wu
share/examples/bioperl/blast/out/blastp.205.gz
share/examples/bioperl/blast/out/blastp.2a.gz
share/examples/bioperl/blast/out/blastp.2b.gz
share/examples/bioperl/blast/out/blastp.email.html.gz
share/examples/bioperl/blast/out/blastx.2
share/examples/bioperl/blast/out/blastx.2.email.gz
share/examples/bioperl/blast/out/blastx.208.gz
share/examples/bioperl/blast/out/tblastn.206.out.gz
share/examples/bioperl/blast/seq/acc1.dna.fasta
share/examples/bioperl/blast/seq/seqs.fasta
share/examples/bioperl/blast/seq/yal011w.dna.fasta
share/examples/bioperl/blast/seq/yel009c.fasta
share/examples/bioperl/blast/seq/ymr284w.fasta
share/examples/bioperl/blast/blast_config.pl
share/examples/bioperl/blast/blast_seq.pl
share/examples/bioperl/blast/example.table1
share/examples/bioperl/blast/example.table2
share/examples/bioperl/blast/html.pl
share/examples/bioperl/blast/parse_blast.pl
share/examples/bioperl/blast/parse_blast2.pl
share/examples/bioperl/blast/parse_multi.pl
share/examples/bioperl/blast/parse_positions.pl
share/examples/bioperl/blast/print_blasts.pl
share/examples/bioperl/blast/retrieve_blast.pl
share/examples/bioperl/blast/run_blast_remote.pl
share/examples/bioperl/blosum62.bla
share/examples/bioperl/change_gene.pl
share/examples/bioperl/clustalw.pl
share/examples/bioperl/getGenBank.pl
share/examples/bioperl/gon250.bla
share/examples/bioperl/gsequence
share/examples/bioperl/hitdisplay.pl
share/examples/bioperl/psw.pl
share/examples/bioperl/restriction.pl
share/examples/bioperl/rev_and_trans.pl
share/examples/bioperl/seq_pattern.pl
share/examples/bioperl/simplealign.pl
share/examples/bioperl/standaloneblast.pl
share/examples/bioperl/test-genscan.pl
share/examples/bioperl/root_object/Outer.pm
share/examples/bioperl/root_object/Bar.pm
share/examples/bioperl/root_object/Foo.pm
share/examples/bioperl/root_object/vector/Person.pm
share/examples/bioperl/root_object/vector/PersonManager.pm
share/examples/bioperl/root_object/vector/vector.out
share/examples/bioperl/root_object/vector/vector.pl
share/examples/bioperl/root_object/destroy.pl
share/examples/bioperl/root_object/error.out
share/examples/bioperl/root_object/error.pl
share/examples/bioperl/root_object/filehandle.out
share/examples/bioperl/root_object/filehandle.pl
share/examples/bioperl/root_object/io.out
share/examples/bioperl/root_object/io.pl
share/examples/bioperl/root_object/read.pl
share/examples/bioperl/root_object/read.test
share/examples/bioperl/root_object/read.test2
share/examples/bioperl/root_object/read.test3
share/examples/bioperl/root_object/utilities.pl
share/examples/bioperl/seq/seq.fasta.gz
share/examples/bioperl/seq/id.list
share/examples/bioperl/seq/seq1.fasta
share/examples/bioperl/seq/seq2.fasta
share/examples/bioperl/seq/seqs1.pl
share/examples/bioperl/seq/seqs2.pl
share/examples/bioperl/seq/seqs3.pl
share/examples/bioperl/seq/seqtools.pl

6
biology/bioperl/distinfo Normal file
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@@ -0,0 +1,6 @@
$NetBSD: distinfo,v 1.4 2006/10/02 21:34:28 rillig Exp $
SHA1 (bioperl-0.7.0.tar.gz) = c86abeeb5f2e2b98d1577d9cefd51ce15bbcb6b6
RMD160 (bioperl-0.7.0.tar.gz) = 41c4162d8d8ec5b406ba34d0d48702700d62108d
Size (bioperl-0.7.0.tar.gz) = 1329985 bytes
SHA1 (patch-aa) = 2e1064f4d7c343cf62f53f2a179a3a1841220dc7

21
biology/bioperl/patches/patch-aa Normal file
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@@ -0,0 +1,21 @@
$NetBSD: patch-aa,v 1.3 2006/10/02 21:34:28 rillig Exp $
If LWP::UserAgent is not available, exit before the module is required
implicitly by Bio::DB::GDB.
--- t/GDB.t.orig 2001-03-01 10:11:15.000000000 +0100
+++ t/GDB.t 2006-10-02 23:30:15.000000000 +0200
@@ -33,10 +33,9 @@ BEGIN {
foreach ( 1..$NUMTESTS) { skip(1,1); }
$error = 1;
}
-}
-
-if( $error == 1 ) {
- exit(0);
+ if( $error == 1 ) {
+ exit(0);
+ }
}
use Bio::DB::GDB;

4
biology/bodr/DESCR Normal file
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@@ -0,0 +1,4 @@
The Blue Obelisk Data Repository lists many important chemoinformatics
data such as element and isotope properties, atomic radii, etc.
including references to original literature. Developers can use
this repository to make their software interoperable.

22
biology/bodr/Makefile Normal file
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@@ -0,0 +1,22 @@
# $NetBSD: Makefile,v 1.5 2013/05/31 12:39:38 wiz Exp $
#
DISTNAME= bodr-9
PKGREVISION= 3
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=bodr/}
MAINTAINER= jihbed.research@gmail.com
HOMEPAGE= http://blueobelisk.org/
COMMENT= Blue Obelisk Data Repository
LICENSE= mit
GNU_CONFIGURE= yes
USE_TOOLS+= pkg-config gmake perl
USE_LANGUAGES= # none
PKGCONFIG_OVERRIDE+= bodr.pc.in
.include "../../textproc/libxml2/buildlink3.mk"
.include "../../textproc/libxslt/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

15
biology/bodr/PLIST Normal file
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@@ -0,0 +1,15 @@
@comment $NetBSD: PLIST,v 1.1.1.1 2011/10/05 22:03:12 ryoon Exp $
share/bodr/crystalstructures.xml
share/bodr/dicts/blueobelisk-dictionary.xml
share/bodr/elements.xml
share/bodr/isotopes.xml
share/bodr/space-groups.xml
share/doc/bodr/AUTHORS
share/doc/bodr/COPYING
share/doc/bodr/ChangeLog
share/doc/bodr/README
share/doc/bodr/THANKS
share/doc/bodr/biblio/crystalstructures_biblio.html
share/doc/bodr/biblio/elements_biblio.html
share/doc/bodr/biblio/space-groups_biblio.html
share/pkgconfig/bodr.pc

13
biology/bodr/buildlink3.mk Normal file
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@@ -0,0 +1,13 @@
# $NetBSD: buildlink3.mk,v 1.1.1.1 2011/10/05 22:03:12 ryoon Exp $
BUILDLINK_TREE+= bodr
.if !defined(BODR_BUILDLINK3_MK)
BODR_BUILDLINK3_MK:=
BUILDLINK_API_DEPENDS.bodr+= bodr>=8
BUILDLINK_PKGSRCDIR.bodr?= ../../biology/bodr
.endif # BODR_BUILDLINK3_MK
BUILDLINK_TREE+= -bodr

5
biology/bodr/distinfo Normal file
View File

@@ -0,0 +1,5 @@
$NetBSD: distinfo,v 1.1.1.1 2011/10/05 22:03:12 ryoon Exp $
SHA1 (bodr-9.tar.gz) = 851502a59d8cd03c0a67f70768f97dc8692b2893
RMD160 (bodr-9.tar.gz) = 9df0c0397f036c9d2f3efc66d3f3b705b5c10b25
Size (bodr-9.tar.gz) = 286732 bytes

6
biology/chemical-mime-data/DESCR Normal file
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@@ -0,0 +1,6 @@
The chemical-mime-data package is a collection of data files to add support
for various chemical MIME types on Linux/UNIX desktops, such as KDE and GNOME.
Chemical MIMEs were proposed in 1995, though it seems they have never been
registered with IANA. But they are widely used and the project's aim is, to
support these important, but unofficial MIME types.

25
biology/chemical-mime-data/Makefile Normal file
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@@ -0,0 +1,25 @@
# $NetBSD: Makefile,v 1.2 2012/09/11 20:32:11 asau Exp $
#
DISTNAME= chemical-mime-data-0.1.94
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=chemical-mime/}
MAINTAINER= kamel.derouiche@gmail.com
HOMEPAGE= http://chemical-mime.sourceforge.net/
COMMENT= Chemical mime and file type support for desktops
LICENSE= gnu-lgpl-v2.1 # or later
BUILD_DEPENDS+= ImageMagick-[0-9]*:../../graphics/ImageMagick
BUILD_DEPENDS+= libxslt-[0-9]*:../../textproc/libxslt
GNU_CONFIGURE= yes
USE_PKGLOCALEDIR= yes
USE_TOOLS+= pkg-config intltool msgfmt gmake
PKGCONFIG_OVERRIDE+= chemical-mime-data.pc.in
.include "../../databases/gnome-mime-data/buildlink3.mk"
.include "../../databases/shared-mime-info/mimedb.mk"
.include "../../graphics/hicolor-icon-theme/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

64
biology/chemical-mime-data/PLIST Normal file
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@@ -0,0 +1,64 @@
@comment $NetBSD: PLIST,v 1.1.1.1 2011/10/05 22:10:57 ryoon Exp $
share/doc/chemical-mime-data/chemical-mime-data.html
share/doc/chemical-mime-data/cmd.css
share/doc/chemical-mime-data/index.html
share/icons/hicolor/128x128/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/16x16/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/192x192/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/22x22/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/24x24/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/32x32/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/36x36/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/48x48/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/64x64/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/72x72/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/96x96/mimetypes/gnome-mime-chemical.png
share/icons/hicolor/scalable/mimetypes/gnome-mime-chemical.svgz
share/locale/de/LC_MESSAGES/chemical-mime-data.mo
share/locale/fr/LC_MESSAGES/chemical-mime-data.mo
share/mime-info/chemical-mime-data.keys
share/mime-info/chemical-mime-data.mime
share/mime/packages/chemical-mime-data.xml
share/mimelnk/chemical/x-alchemy.desktop
share/mimelnk/chemical/x-cache.desktop
share/mimelnk/chemical/x-cactvs-ascii.desktop
share/mimelnk/chemical/x-cactvs-binary.desktop
share/mimelnk/chemical/x-cactvs-table.desktop
share/mimelnk/chemical/x-cdx.desktop
share/mimelnk/chemical/x-cdxml.desktop
share/mimelnk/chemical/x-chem3d.desktop
share/mimelnk/chemical/x-cif.desktop
share/mimelnk/chemical/x-cml.desktop
share/mimelnk/chemical/x-dmol.desktop
share/mimelnk/chemical/x-gamess-input.desktop
share/mimelnk/chemical/x-gamess-output.desktop
share/mimelnk/chemical/x-gaussian-input.desktop
share/mimelnk/chemical/x-gaussian-log.desktop
share/mimelnk/chemical/x-genbank.desktop
share/mimelnk/chemical/x-gulp.desktop
share/mimelnk/chemical/x-hin.desktop
share/mimelnk/chemical/x-inchi-xml.desktop
share/mimelnk/chemical/x-inchi.desktop
share/mimelnk/chemical/x-jcamp-dx.desktop
share/mimelnk/chemical/x-macromodel-input.desktop
share/mimelnk/chemical/x-mdl-molfile.desktop
share/mimelnk/chemical/x-mdl-rdfile.desktop
share/mimelnk/chemical/x-mdl-rxnfile.desktop
share/mimelnk/chemical/x-mdl-tgf.desktop
share/mimelnk/chemical/x-mmcif.desktop
share/mimelnk/chemical/x-mol2.desktop
share/mimelnk/chemical/x-mopac-graph.desktop
share/mimelnk/chemical/x-mopac-out.desktop
share/mimelnk/chemical/x-msi-car.desktop
share/mimelnk/chemical/x-msi-hessian.desktop
share/mimelnk/chemical/x-msi-mdf.desktop
share/mimelnk/chemical/x-msi-msi.desktop
share/mimelnk/chemical/x-ncbi-asn1-binary.desktop
share/mimelnk/chemical/x-ncbi-asn1-xml.desktop
share/mimelnk/chemical/x-ncbi-asn1.desktop
share/mimelnk/chemical/x-shelx.desktop
share/mimelnk/chemical/x-vmd.desktop
share/mimelnk/chemical/x-xyz.desktop
share/pixmaps/chemistry.png
share/pixmaps/gnome-mime-chemical.png
share/pkgconfig/chemical-mime-data.pc

13
biology/chemical-mime-data/buildlink3.mk Normal file
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@@ -0,0 +1,13 @@
# $NetBSD: buildlink3.mk,v 1.2 2011/10/07 03:57:23 dholland Exp $
BUILDLINK_TREE+= chemical-mime-data
.if !defined(CHEMICAL_MIME_DATA_BUILDLINK3_MK)
CHEMICAL_MIME_DATA_BUILDLINK3_MK:=
BUILDLINK_API_DEPENDS.chemical-mime-data+= chemical-mime-data>=0.1.94
BUILDLINK_PKGSRCDIR.chemical-mime-data?= ../../biology/chemical-mime-data
.endif # CHEMICAL_MIME_DATA_BUILDLINK3_MK
BUILDLINK_TREE+= -chemical-mime-data

5
biology/chemical-mime-data/distinfo Normal file
View File

@@ -0,0 +1,5 @@
$NetBSD: distinfo,v 1.1.1.1 2011/10/05 22:10:56 ryoon Exp $
SHA1 (chemical-mime-data-0.1.94.tar.gz) = 4e6568080b3db9a9978ab28b35ee64db96190900
RMD160 (chemical-mime-data-0.1.94.tar.gz) = e44e21e5ff3b95af17376c7b4317c49ddae64153
Size (chemical-mime-data-0.1.94.tar.gz) = 193359 bytes

7
biology/chemtool/DESCR Normal file
View File

@@ -0,0 +1,7 @@
Chemtool is a program for drawing organic molecules easily and store
them as a X bitmap file. It runs under the X Window System using the
GTK widget set.
Molecules can be exported in X bitmap format. Encapsulated postscript,
fig, or PicTeX formats are also possible if the fig2dev program from
the transfig package (pkgsrc/print/transfig/) is installed.

27
biology/chemtool/Makefile Normal file
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@@ -0,0 +1,27 @@
# $NetBSD: Makefile,v 1.46 2013/06/06 12:54:06 wiz Exp $
DISTNAME= chemtool-1.6.13
PKGREVISION= 10
CATEGORIES= biology
MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
MAINTAINER= pkgsrc-users@NetBSD.org
HOMEPAGE= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
COMMENT= Program for drawing organic molecules
PKG_INSTALLATION_TYPES= overwrite pkgviews
USE_PKGLOCALEDIR= yes
USE_TOOLS+= gmake pkg-config
GNU_CONFIGURE= yes
CONFIGURE_ARGS+= --without-gnomedir
INSTALLATION_DIRS= share/doc/chemtool share/examples/chemtool
post-install:
${INSTALL_DATA} ${WRKSRC}/examples/* ${DESTDIR}${PREFIX}/share/examples/chemtool
cd ${WRKSRC} && ${INSTALL_DATA} README TODO \
${DESTDIR}${PREFIX}/share/doc/chemtool/
.include "../../x11/gtk2/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

54
biology/chemtool/PLIST Normal file
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@@ -0,0 +1,54 @@
@comment $NetBSD: PLIST,v 1.9 2009/09/05 13:43:26 asau Exp $
bin/chemtool
bin/chemtoolbg
bin/cht
man/man1/chemtool.1
man/man1/cht.1
share/doc/chemtool/README
share/doc/chemtool/TODO
share/examples/chemtool/14263232.mol
share/examples/chemtool/AMP.cht
share/examples/chemtool/Adenosine.cht
share/examples/chemtool/Dehydrotubifolin.cht
share/examples/chemtool/G-host.pdb
share/examples/chemtool/Indolizomycin.cht
share/examples/chemtool/Lepicidin-A-Aglycon.cht
share/examples/chemtool/Neu2
share/examples/chemtool/amine.mol
share/examples/chemtool/anabsinthin.cht
share/examples/chemtool/anthocyanidine.cht
share/examples/chemtool/atp.cht
share/examples/chemtool/bcarotin.pdb
share/examples/chemtool/breve.cht
share/examples/chemtool/bufotalin.cht
share/examples/chemtool/byrostatin1.cht
share/examples/chemtool/c70.cht
share/examples/chemtool/camphor.cht
share/examples/chemtool/chlorophyll.cht
share/examples/chemtool/claisen.cht
share/examples/chemtool/dodecahedran.cht
share/examples/chemtool/indigo.cht
share/examples/chemtool/kdo.cht
share/examples/chemtool/krebs.cht
share/examples/chemtool/labeltest
share/examples/chemtool/pagodan.cht
share/examples/chemtool/penicillin_v.cht
share/examples/chemtool/pteridin.cht
share/examples/chemtool/reaction.cht
share/examples/chemtool/rutamycin_b.cht
share/examples/chemtool/sample.sdf
share/examples/chemtool/tbutylazulene.cht
share/examples/chemtool/tcdd.cht
share/examples/chemtool/tetracyclin.cht
share/examples/chemtool/textsizes.cht
share/examples/chemtool/v3000.mol
share/examples/chemtool/viagra.cht
share/locale/bg/LC_MESSAGES/chemtool.mo
share/locale/cs/LC_MESSAGES/chemtool.mo
share/locale/de/LC_MESSAGES/chemtool.mo
share/locale/fr/LC_MESSAGES/chemtool.mo
share/locale/nl/LC_MESSAGES/chemtool.mo
share/locale/pl/LC_MESSAGES/chemtool.mo
share/locale/pt_BR/LC_MESSAGES/chemtool.mo
share/locale/pt_PT/LC_MESSAGES/chemtool.mo
share/locale/ru/LC_MESSAGES/chemtool.mo

5
biology/chemtool/distinfo Normal file
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@@ -0,0 +1,5 @@
$NetBSD: distinfo,v 1.14 2012/01/08 12:47:18 ryoon Exp $
SHA1 (chemtool-1.6.13.tar.gz) = 03d139cfefe9e4e8957239d8d16c56dc6a369090
RMD160 (chemtool-1.6.13.tar.gz) = c54494fdda19deb0115839263c7db5b9825bf56b
Size (chemtool-1.6.13.tar.gz) = 838868 bytes

5
biology/clustalw/DESCR Normal file
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@@ -0,0 +1,5 @@
Clustal W is a general purpose multiple alignment program for
DNA or proteins. Clustal W can write various output files in
Phylip format. Furthermore, Clustal W is capable of producing
phylogenetic trees from multiple sequence alignments in the GCG
MSF Format.

20
biology/clustalw/Makefile Normal file
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@@ -0,0 +1,20 @@
# $NetBSD: Makefile,v 1.13 2012/12/13 13:27:13 wen Exp $
DISTNAME= clustalw-2.1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/ \
http://www.clustal.org/download/current/
MAINTAINER= babafou@babafou.eu.org
HOMEPAGE= http://bips.u-strasbg.fr/fr/Documentation/ClustalW/
COMMENT= General purpose multiple alignment program for DNA or proteins
LICENSE= gnu-gpl-v3 AND gnu-lgpl-v3
PKG_INSTALLATION_TYPES= overwrite pkgviews
GNU_CONFIGURE= yes
USE_LANGUAGES= c c++
INSTALLATION_DIRS= bin
.include "../../mk/bsd.pkg.mk"

2
biology/clustalw/PLIST Normal file
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@@ -0,0 +1,2 @@
@comment $NetBSD: PLIST,v 1.3 2012/12/13 13:27:13 wen Exp $
bin/clustalw2

6
biology/clustalw/distinfo Normal file
View File

@@ -0,0 +1,6 @@
$NetBSD: distinfo,v 1.7 2013/04/29 21:31:09 joerg Exp $
SHA1 (clustalw-2.1.tar.gz) = f29784f68585544baa77cbeca6392e533d4cf433
RMD160 (clustalw-2.1.tar.gz) = e193769955a6270797fcb039ca398a4b59d9248d
Size (clustalw-2.1.tar.gz) = 350761 bytes
SHA1 (patch-src_general_VectorOutOfRange.h) = 8c1d3df314efba8afa88410542e26881951e7193

12
biology/clustalw/patches/patch-src_general_VectorOutOfRange.h Normal file
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@@ -0,0 +1,12 @@
$NetBSD: patch-src_general_VectorOutOfRange.h,v 1.1 2013/04/29 21:31:10 joerg Exp $
--- src/general/VectorOutOfRange.h.orig 2013-04-29 20:21:11.000000000 +0000
+++ src/general/VectorOutOfRange.h
@@ -4,6 +4,7 @@
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#include <stdexcept>
+#include <string>
#include <exception>
namespace clustalw
{

3
biology/coalesce/DESCR Normal file
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@@ -0,0 +1,3 @@
COALESCE fits the model which has a single population of constant size, and
estimates 4Nu, where N is the effective population size and u is the neutral
mutation rate per site.

34
biology/coalesce/Makefile Normal file
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@@ -0,0 +1,34 @@
# $NetBSD: Makefile,v 1.9 2012/09/11 20:32:11 asau Exp $
#
DISTNAME= coalesce1.5b
PKGNAME= coalesce-1.5.0.2
CATEGORIES= biology
MASTER_SITES= http://evolution.genetics.washington.edu/lamarc/coalesce/
MAINTAINER= brook@nmsu.edu
HOMEPAGE= http://evolution.genetics.washington.edu/lamarc/coalesce.html
COMMENT= Estimates effective population size and mutation rate
WRKSRC= ${WRKDIR}/coalesce1.5beta
BUILD_TARGET= coalesce
DOCDIR= ${PREFIX}/share/doc/coalesce
EXDIR= ${PREFIX}/share/examples/coalesce
DOCFILES= coalesce.doc errors.doc readme
EXFILES= bestree infile intree outfile parmfile seedfile
INSTALLATION_DIRS= bin
do-install:
${INSTALL_DATA_DIR} ${DESTDIR}${DOCDIR}
${INSTALL_DATA_DIR} ${DESTDIR}${EXDIR}
${INSTALL_PROGRAM} ${WRKSRC}/coalesce ${DESTDIR}${PREFIX}/bin
for f in ${DOCFILES}; do \
${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${DOCDIR}/$$f; \
done
for f in ${EXFILES}; do \
${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${EXDIR}/$$f; \
done
.include "../../mk/bsd.pkg.mk"

11
biology/coalesce/PLIST Normal file
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@@ -0,0 +1,11 @@
@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
bin/coalesce
share/doc/coalesce/coalesce.doc
share/doc/coalesce/errors.doc
share/doc/coalesce/readme
share/examples/coalesce/bestree
share/examples/coalesce/infile
share/examples/coalesce/intree
share/examples/coalesce/outfile
share/examples/coalesce/parmfile
share/examples/coalesce/seedfile

6
biology/coalesce/distinfo Normal file
View File

@@ -0,0 +1,6 @@
$NetBSD: distinfo,v 1.2 2005/02/22 21:28:55 agc Exp $
SHA1 (coalesce1.5b.tar.gz) = ec2a13da25474440a0c57b2a2e634c94db30961e
RMD160 (coalesce1.5b.tar.gz) = 199a0f219413ea67feea98a6864f43373d3955bc
Size (coalesce1.5b.tar.gz) = 46153 bytes
SHA1 (patch-aa) = b4c3afcb563c54d4b16f20f8b4b9fc649b49deee

31
biology/coalesce/patches/patch-aa Normal file
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@@ -0,0 +1,31 @@
$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $
--- Makefile.orig 1996-02-29 11:00:09.000000000 -0500
+++ Makefile 2003-09-29 20:51:32.000000000 -0400
@@ -1,20 +1,20 @@
LIBS = -lm
BINDIR = ./bin
-CFLAGS = -g
-CC = cc $(CFLAGS)
+#CFLAGS = -g
+#CC = cc $(CFLAGS)
DCC = gcc -g -DDMALLOC_FUNC_CHECK -ansi -pedantic
DLIBS = -lm -L/usr/local/lib -ldmalloc
# -O
PROGS = coalesce fluctuate
coalesce : coalesce.c constants.h lamarc.h
- $(CC) coalesce.c $(LIBS) -o coalesce
+ $(CC) ${CFLAGS} coalesce.c ${LDFLAGS} $(LIBS) -o coalesce
modellike.o : modellike.c
- $(CC) -c modellike.c
+ $(CC) ${CFLAGS} -c modellike.c
fluctuate.o : fluctuate.c
- $(CC) -c fluctuate.c
+ $(CC) ${CFLAGS} -c fluctuate.c
fluctuate : fluctuate.o modellike.o
- $(CC) fluctuate.o modellike.o $(LIBS) -o fluctuate
+ $(CC) ${CFLAGS} fluctuate.o modellike.o ${LDFLAGS} $(LIBS) -o fluctuate

8
biology/fastDNAml/DESCR Normal file
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@@ -0,0 +1,8 @@
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
(part of his PHYLIP package). Users should consult the documentation for
DNAML before using this program.
fastDNAml is an attempt to solve the same problem as DNAML, but to do so
faster and using less memory, so that larger trees and/or more bootstrap
replicates become tractable. Much of fastDNAml is merely a recoding of the
PHYLIP 3.3 DNAML program from PASCAL to C.

35
biology/fastDNAml/Makefile Normal file
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@@ -0,0 +1,35 @@
# $NetBSD: Makefile,v 1.10 2012/09/11 20:32:12 asau Exp $
DISTNAME= fastDNAml_1.2.2
PKGNAME= fastDNAml-1.2.2
CATEGORIES= biology
MASTER_SITES= http://geta.life.uiuc.edu/~gary/programs/fastDNAml/
MAINTAINER= babafou@babafou.eu.org
HOMEPAGE= http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
COMMENT= Program derived from Joseph Felsenstein's version 3.3 DNAML
WRKSRC= ${WRKDIR}/${DISTNAME}/source
INSTALLATION_DIRS= bin
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/fastDNAml ${DESTDIR}${PREFIX}/bin
.for SCRIPT in ae2dnaml bootstrap categories categories_file \
checkpoint_summary clean_checkpoints clean_jumbles \
dnaml_progress fastDNAml_boot fastDNAml_loop \
frequencies global iterate_rates jumble min_info \
n_categories n_files out.PID outgroup printdata \
quickadd restart scores transition treefile \
treefile2prolog trees2NEXUS trees2prolog userlengths \
usertree usertrees weights weights_categories
${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/scripts/${SCRIPT} \
${DESTDIR}${PREFIX}/bin
.endfor
${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/fastDNAml
.for DOC in fastDNAml_doc_1.2.txt fastDNAml_scripts.txt
${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/docs/${DOC} \
${DESTDIR}${PREFIX}/share/doc/fastDNAml
.endfor
.include "../../mk/bsd.pkg.mk"

37
biology/fastDNAml/PLIST Normal file
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@@ -0,0 +1,37 @@
@comment $NetBSD: PLIST,v 1.3 2009/06/14 17:34:33 joerg Exp $
bin/ae2dnaml
bin/bootstrap
bin/categories
bin/categories_file
bin/checkpoint_summary
bin/clean_checkpoints
bin/clean_jumbles
bin/dnaml_progress
bin/fastDNAml
bin/fastDNAml_boot
bin/fastDNAml_loop
bin/frequencies
bin/global
bin/iterate_rates
bin/jumble
bin/min_info
bin/n_categories
bin/n_files
bin/out.PID
bin/outgroup
bin/printdata
bin/quickadd
bin/restart
bin/scores
bin/transition
bin/treefile
bin/treefile2prolog
bin/trees2NEXUS
bin/trees2prolog
bin/userlengths
bin/usertree
bin/usertrees
bin/weights
bin/weights_categories
share/doc/fastDNAml/fastDNAml_doc_1.2.txt
share/doc/fastDNAml/fastDNAml_scripts.txt

5
biology/fastDNAml/distinfo Normal file
View File

@@ -0,0 +1,5 @@
$NetBSD: distinfo,v 1.4 2005/02/22 21:28:55 agc Exp $
SHA1 (fastDNAml_1.2.2.tar.gz) = 78197cbd760163f65085ac80c36d4286a1f29e34
RMD160 (fastDNAml_1.2.2.tar.gz) = 1ded8fe0c9621d9fb2f6f090a97d16fbdf8e18bf
Size (fastDNAml_1.2.2.tar.gz) = 70005 bytes

5
biology/fluctuate/DESCR Normal file
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@@ -0,0 +1,5 @@
FLUCTUATE fits the model which has a single population which has been
growing (or shrinking) according to an exponential growth law. It
estimates 4Nu and g, where N is the effective population size, u is
the neutral mutation rate per site, and g is the growth rate of the
population.

9
biology/fluctuate/MESSAGE Normal file
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@@ -0,0 +1,9 @@
===========================================================================
$NetBSD: MESSAGE,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $
In order to run the fluctuate example, you should create a directory for
example files and then copy ${PREFIX}/share/examples/fluctuate/{bestree,
infile,outfile} to there. After that, you can simply run 'fluctuate' from
that directory.
===========================================================================

34
biology/fluctuate/Makefile Normal file
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@@ -0,0 +1,34 @@
# $NetBSD: Makefile,v 1.9 2012/09/11 20:32:12 asau Exp $
#
DISTNAME= fluctuate1.4.src.doc
PKGNAME= fluctuate-1.4
CATEGORIES= biology
MASTER_SITES= http://evolution.gs.washington.edu/lamarc/fluctuate/
MAINTAINER= brook@nmsu.edu
HOMEPAGE= http://evolution.genetics.washington.edu/lamarc/fluctuate.html
COMMENT= Estimation of population growth rate
WRKSRC= ${WRKDIR}/fluctuate1.4
BUILD_TARGET= fluctuate
DOCDIR= ${PREFIX}/share/doc/fluctuate
EXDIR= ${PREFIX}/share/examples/fluctuate
DOCFILES= fluctuate.doc errors.doc
EXFILES= bestree infile outfile
INSTALLATION_DIRS= bin
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/fluctuate ${DESTDIR}${PREFIX}/bin
${INSTALL_DATA_DIR} ${DESTDIR}${DOCDIR}
${INSTALL_DATA_DIR} ${DESTDIR}${EXDIR}
for f in ${DOCFILES}; do \
${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${DOCDIR}/$$f; \
done
for f in ${EXFILES}; do \
${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${EXDIR}/$$f; \
done
.include "../../mk/bsd.pkg.mk"

7
biology/fluctuate/PLIST Normal file
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@@ -0,0 +1,7 @@
@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
bin/fluctuate
share/doc/fluctuate/errors.doc
share/doc/fluctuate/fluctuate.doc
share/examples/fluctuate/bestree
share/examples/fluctuate/infile
share/examples/fluctuate/outfile

6
biology/fluctuate/distinfo Normal file
View File

@@ -0,0 +1,6 @@
$NetBSD: distinfo,v 1.2 2005/02/22 21:28:55 agc Exp $
SHA1 (fluctuate1.4.src.doc.tar.gz) = 7e9fb766312237f85a191327aae37c9a52a2e408
RMD160 (fluctuate1.4.src.doc.tar.gz) = 39b11f768ad148319cefdee8058017c31d5ef14c
Size (fluctuate1.4.src.doc.tar.gz) = 70690 bytes
SHA1 (patch-aa) = d7637d2d2b47d9ceb920319393f13e84a60bfae0

45
biology/fluctuate/patches/patch-aa Normal file
View File

@@ -0,0 +1,45 @@
$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:19:32 jschauma Exp $
--- Makefile.orig 2003-09-29 21:08:30.000000000 -0400
+++ Makefile 2003-09-29 21:09:31.000000000 -0400
@@ -1,30 +1,30 @@
LIBS = -lm
BINDIR = ./bin
-CFLAGS = -O2 -funroll-loops
-CC = gcc $(CFLAGS)
+CFLAGS += -O2 -funroll-loops
+#CC = gcc $(CFLAGS)
fluctuate : fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
coal_modellike.o
- $(CC) fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
- coal_modellike.o $(LIBS) -o fluctuate
+ $(CC) ${CFLAGS} fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
+ coal_modellike.o ${LDFLAGS} $(LIBS) -o fluctuate
clean :
rm fluctuate.o fluc_modellike.o coal_modellike.o getdata.o plot.o wrap.o
fluctuate.o : fluctuate.c
- $(CC) -c fluctuate.c
+ $(CC) ${CFLAGS} -c fluctuate.c
fluc_modellike.o : fluc_modellike.c
- $(CC) -c fluc_modellike.c
+ $(CC) ${CFLAGS} -c fluc_modellike.c
coal_modellike.o : coal_modellike.c
- $(CC) -c coal_modellike.c
+ $(CC) ${CFLAGS} -c coal_modellike.c
getdata.o : getdata.c
- $(CC) -c getdata.c
+ $(CC) ${CFLAGS} -c getdata.c
plot.o : plot.c
- $(CC) -c plot.c
+ $(CC) ${CFLAGS} -c plot.c
wrap.o : wrap.c
- $(CC) -c wrap.c
+ $(CC) ${CFLAGS} -c wrap.c

4
biology/genesplicer/DESCR Normal file
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@@ -0,0 +1,4 @@
GeneSplicer is a fast, flexible system for detecting splice sites in the
genomic DNA of various eukaryotes. The system has been trained and tested
successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human,
Drosophila, and rice.

32
biology/genesplicer/Makefile Normal file
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@@ -0,0 +1,32 @@
# $NetBSD: Makefile,v 1.13 2013/04/06 13:24:18 rodent Exp $
#
DISTNAME= GeneSplicer
PKGNAME= genesplicer-20030403
CATEGORIES= biology
MASTER_SITES= ftp://ftp.tigr.org/pub/software/GeneSplicer/
MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= ftp://ftp.tigr.org/pub/software/GeneSplicer/
COMMENT= Computational Method for Splice Site Prediction
USE_LANGUAGES= c c++
USE_TOOLS+= pax
EXDIR= ${PREFIX}/share/examples/genesplicer
EXAMPLES= arabidopsis drosophila malaria pyoelii human rice \
training_data_sets/Arabidopsis \
training_data_sets/Human
MAKE_FILE= makefile
BUILD_DIRS= sources
INSTALLATION_DIRS= bin
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/sources/genesplicer ${DESTDIR}${PREFIX}/bin
${INSTALL_DATA_DIR} ${DESTDIR}${EXDIR}
.for doc in readme fasta.example fasta.results
${INSTALL_DATA} ${WRKSRC}/sources/${doc} ${DESTDIR}${EXDIR}
.endfor
cd ${WRKSRC} && pax -rw ${EXAMPLES} ${DESTDIR}${EXDIR}
.include "../../mk/bsd.pkg.mk"

138
biology/genesplicer/PLIST Normal file
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@@ -0,0 +1,138 @@
@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
bin/genesplicer
share/examples/genesplicer/arabidopsis/acc1.mar
share/examples/genesplicer/arabidopsis/acc15
share/examples/genesplicer/arabidopsis/acc16
share/examples/genesplicer/arabidopsis/acc22
share/examples/genesplicer/arabidopsis/acc24
share/examples/genesplicer/arabidopsis/acc25
share/examples/genesplicer/arabidopsis/acc26
share/examples/genesplicer/arabidopsis/acc6
share/examples/genesplicer/arabidopsis/acc7
share/examples/genesplicer/arabidopsis/acc8
share/examples/genesplicer/arabidopsis/config_file
share/examples/genesplicer/arabidopsis/don1.mar
share/examples/genesplicer/arabidopsis/don13
share/examples/genesplicer/arabidopsis/don14
share/examples/genesplicer/arabidopsis/don19
share/examples/genesplicer/arabidopsis/don20
share/examples/genesplicer/arabidopsis/don23
share/examples/genesplicer/arabidopsis/don24
share/examples/genesplicer/arabidopsis/don7
share/examples/genesplicer/arabidopsis/don8
share/examples/genesplicer/arabidopsis/exons.dat
share/examples/genesplicer/arabidopsis/f.acc
share/examples/genesplicer/arabidopsis/f.don
share/examples/genesplicer/arabidopsis/outex
share/examples/genesplicer/arabidopsis/outin
share/examples/genesplicer/arabidopsis/score_ex.acc
share/examples/genesplicer/arabidopsis/score_ex.don
share/examples/genesplicer/arabidopsis/score_in.acc
share/examples/genesplicer/arabidopsis/score_in.don
share/examples/genesplicer/arabidopsis/seqs
share/examples/genesplicer/drosophila/acc1.mar
share/examples/genesplicer/drosophila/acc2
share/examples/genesplicer/drosophila/acc3
share/examples/genesplicer/drosophila/acc4
share/examples/genesplicer/drosophila/config_file
share/examples/genesplicer/drosophila/don1.mar
share/examples/genesplicer/drosophila/don2
share/examples/genesplicer/drosophila/don4
share/examples/genesplicer/drosophila/don5
share/examples/genesplicer/drosophila/don6
share/examples/genesplicer/drosophila/exons.dat
share/examples/genesplicer/drosophila/f.acc
share/examples/genesplicer/drosophila/f.don
share/examples/genesplicer/drosophila/false.filter.acc
share/examples/genesplicer/drosophila/false.filter.don
share/examples/genesplicer/drosophila/false.nofilter.acc
share/examples/genesplicer/drosophila/false.nofilter.don
share/examples/genesplicer/drosophila/outex
share/examples/genesplicer/drosophila/outin
share/examples/genesplicer/drosophila/score_ex.acc
share/examples/genesplicer/drosophila/score_ex.don
share/examples/genesplicer/drosophila/score_in.acc
share/examples/genesplicer/drosophila/score_in.don
share/examples/genesplicer/drosophila/seqs
share/examples/genesplicer/fasta.example
share/examples/genesplicer/fasta.results
share/examples/genesplicer/human/acc1.mar
share/examples/genesplicer/human/acc13
share/examples/genesplicer/human/acc14
share/examples/genesplicer/human/acc19
share/examples/genesplicer/human/acc20
share/examples/genesplicer/human/acc25
share/examples/genesplicer/human/acc26
share/examples/genesplicer/human/acc32
share/examples/genesplicer/human/acc33
share/examples/genesplicer/human/acc34
share/examples/genesplicer/human/acc7
share/examples/genesplicer/human/acc8
share/examples/genesplicer/human/chgd.fasta
share/examples/genesplicer/human/config_file
share/examples/genesplicer/human/don1.mar
share/examples/genesplicer/human/don10
share/examples/genesplicer/human/don15
share/examples/genesplicer/human/don16
share/examples/genesplicer/human/don19
share/examples/genesplicer/human/don2
share/examples/genesplicer/human/don20
share/examples/genesplicer/human/don23
share/examples/genesplicer/human/don24
share/examples/genesplicer/human/don9
share/examples/genesplicer/human/embls.seq
share/examples/genesplicer/human/exons.dat
share/examples/genesplicer/human/exons.list
share/examples/genesplicer/human/f.acc
share/examples/genesplicer/human/f.don
share/examples/genesplicer/human/outex
share/examples/genesplicer/human/outin
share/examples/genesplicer/human/score_ex.acc
share/examples/genesplicer/human/score_ex.don
share/examples/genesplicer/human/score_in.acc
share/examples/genesplicer/human/score_in.don
share/examples/genesplicer/human/seqs
share/examples/genesplicer/malaria/acc1.mar
share/examples/genesplicer/malaria/config_file
share/examples/genesplicer/malaria/don1.mar
share/examples/genesplicer/malaria/f.acc
share/examples/genesplicer/malaria/f.don
share/examples/genesplicer/malaria/false.filter.acc
share/examples/genesplicer/malaria/false.filter.don
share/examples/genesplicer/malaria/false.nofilter.acc
share/examples/genesplicer/malaria/false.nofilter.don
share/examples/genesplicer/malaria/score_ex.acc
share/examples/genesplicer/malaria/score_ex.don
share/examples/genesplicer/malaria/score_in.acc
share/examples/genesplicer/malaria/score_in.don
share/examples/genesplicer/pyoelii/acc1
share/examples/genesplicer/pyoelii/acc1.mar
share/examples/genesplicer/pyoelii/acc2
share/examples/genesplicer/pyoelii/config_file
share/examples/genesplicer/pyoelii/don1
share/examples/genesplicer/pyoelii/don1.mar
share/examples/genesplicer/pyoelii/don2
share/examples/genesplicer/pyoelii/f.acc
share/examples/genesplicer/pyoelii/f.don
share/examples/genesplicer/pyoelii/outex
share/examples/genesplicer/pyoelii/outin
share/examples/genesplicer/pyoelii/score_ex.acc
share/examples/genesplicer/pyoelii/score_ex.don
share/examples/genesplicer/pyoelii/score_in.acc
share/examples/genesplicer/pyoelii/score_in.don
share/examples/genesplicer/readme
share/examples/genesplicer/rice/acc1.mar
share/examples/genesplicer/rice/config_file
share/examples/genesplicer/rice/don1.mar
share/examples/genesplicer/rice/exons.dat
share/examples/genesplicer/rice/f.acc
share/examples/genesplicer/rice/f.don
share/examples/genesplicer/rice/score_ex.acc
share/examples/genesplicer/rice/score_ex.don
share/examples/genesplicer/rice/score_in.acc
share/examples/genesplicer/rice/score_in.don
share/examples/genesplicer/rice/seqs
share/examples/genesplicer/training_data_sets/Arabidopsis/exons.dat.nohomologs
share/examples/genesplicer/training_data_sets/Arabidopsis/seqs.nohomologs
share/examples/genesplicer/training_data_sets/Human/exons.dat.nohomologs
share/examples/genesplicer/training_data_sets/Human/seqs.nohomologs

7
biology/genesplicer/distinfo Normal file
View File

@@ -0,0 +1,7 @@
$NetBSD: distinfo,v 1.4 2012/11/16 00:31:35 joerg Exp $
SHA1 (GeneSplicer.tar.gz) = 2be13d1a3ccb108e3e209ca5e66cd5a46e023198
RMD160 (GeneSplicer.tar.gz) = 7ada20a18c742ca259a208ac5ea6fd53fd41a2c4
Size (GeneSplicer.tar.gz) = 9278730 bytes
SHA1 (patch-aa) = 49823d73c45088f599ce288e9d1adb7917f20a3a
SHA1 (patch-sources_genesplicer.cpp) = 3bb032f527b692eb265d7006a7a7519ba79e8cc3

21
biology/genesplicer/patches/patch-aa Normal file
View File

@@ -0,0 +1,21 @@
$NetBSD: patch-aa,v 1.2 2005/11/03 19:36:39 rillig Exp $
--- sources/makefile.orig 2003-09-29 21:39:36.000000000 -0400
+++ sources/makefile 2003-09-29 21:40:57.000000000 -0400
@@ -1,12 +1,12 @@
-CC=g++
+#CC=g++
all: genesplicer
genesplicer: genesplicer.o sites.o
- $(CC) -o genesplicer genesplicer.o sites.o -lm
+ $(CXX) ${CXXFLAGS} -o genesplicer genesplicer.o sites.o ${LDFLAGS} -lm
genesplicer.o: genesplicer.cpp
- $(CC) -c genesplicer.cpp
+ $(CXX) ${CXXFLAGS} -c genesplicer.cpp
sites.o: sites.c
- $(CC) -c sites.c
+ $(CXX) ${CXXFLAGS} -c sites.c

13
biology/genesplicer/patches/patch-sources_genesplicer.cpp Normal file
View File

@@ -0,0 +1,13 @@
$NetBSD: patch-sources_genesplicer.cpp,v 1.1 2012/11/16 00:31:35 joerg Exp $
--- sources/genesplicer.cpp.orig 2012-11-15 13:01:00.000000000 +0000
+++ sources/genesplicer.cpp
@@ -54,7 +54,7 @@ FILE * File_Open (const char *, const
void LoadData(FILE *,char *);
void Process_Options (int, char * []);
-
+int
main (int argc, char * argv [])
{
FILE * fp, *ofp;

6
biology/glimmer/DESCR Normal file
View File

@@ -0,0 +1,6 @@
Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
genes in microbial DNA, especially the genomes of bacteria and archaea.
Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
and distinguish them from noncoding DNA. The IMM approach uses a combination
of Markov models from 1st through 8th-order, weighting each model according to
its predictive power.

36
biology/glimmer/Makefile Normal file
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@@ -0,0 +1,36 @@
# $NetBSD: Makefile,v 1.13 2013/04/06 13:24:18 rodent Exp $
#
DISTNAME= glimmer213
PKGREVISION= 1
PKGNAME= glimmer-2.13
CATEGORIES= biology
MASTER_SITES= ftp://ftp.tigr.org/pub/software/Glimmer/
MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= ftp://ftp.tigr.org/pub/software/Glimmer/
COMMENT= System for finding genes in microbial DNA
CONFLICTS+= generate-[0-9]*
USE_LANGUAGES= c c++
WRKSRC= ${WRKDIR}/glimmer2.13
INSTALLATION_DIRS= bin
do-install:
.for program in adjust anomaly build-icm check codon-usage compare-lists \
generate get-len get-putative glimmer2 long-orfs
${INSTALL_PROGRAM} ${WRKSRC}/${program} ${DESTDIR}${PREFIX}/bin
.endfor
# ``extract'' is also in the csound package, so rename to avoid conflict
${INSTALL_PROGRAM} ${WRKSRC}/extract ${DESTDIR}${PREFIX}/bin/glextract
${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/glimmer
${CP} ${WRKSRC}/README ${WRKSRC}/run-glimmer2.readme
.for doc in run-glimmer2.readme build-icm.readme extract.readme glimmer2.readme long-orfs.readme
${INSTALL_DATA} ${WRKSRC}/${doc} ${DESTDIR}${PREFIX}/share/doc/glimmer
.endfor
${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/glimmer
${INSTALL_SCRIPT} ${WRKSRC}/run-glimmer2 ${DESTDIR}${PREFIX}/share/glimmer
.include "../../mk/bsd.pkg.mk"

19
biology/glimmer/PLIST Normal file
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@@ -0,0 +1,19 @@
@comment $NetBSD: PLIST,v 1.3 2009/06/14 17:34:33 joerg Exp $
bin/adjust
bin/anomaly
bin/build-icm
bin/check
bin/codon-usage
bin/compare-lists
bin/glextract
bin/generate
bin/get-len
bin/get-putative
bin/glimmer2
bin/long-orfs
share/doc/glimmer/build-icm.readme
share/doc/glimmer/extract.readme
share/doc/glimmer/glimmer2.readme
share/doc/glimmer/long-orfs.readme
share/doc/glimmer/run-glimmer2.readme
share/glimmer/run-glimmer2

7
biology/glimmer/distinfo Normal file
View File

@@ -0,0 +1,7 @@
$NetBSD: distinfo,v 1.4 2005/02/22 21:28:55 agc Exp $
SHA1 (glimmer213.tar.gz) = 772752c3c1543066e4c156e5ec0a2e4f0a24c688
RMD160 (glimmer213.tar.gz) = 1667d04bc66f373d5df395e16b79b07814d3ea2c
Size (glimmer213.tar.gz) = 79858 bytes
SHA1 (patch-aa) = ceb45f887c32e91bd96b9d2c8dae39c9cc6fc658
SHA1 (patch-ab) = e2afaa9ff8e0d4a2647a77bbf7e1ba4012d53061

17
biology/glimmer/patches/patch-aa Normal file
View File

@@ -0,0 +1,17 @@
$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
--- Makefile.orig 2003-09-29 22:02:13.000000000 -0400
+++ Makefile 2003-09-29 22:02:45.000000000 -0400
@@ -4,9 +4,9 @@
PROJECTDIR = .
BINDIR = $(PROJECTDIR)
-CC = gcc
-CPPC = g++
-CFLAGS = -O3 -g -Wall
+#CC = gcc
+CPPC = ${CXX}
+#CFLAGS = -O3 -g -Wall
LDFLAGS = -lm
DEPEND_FILES = *.cc *.c *.h

25
biology/glimmer/patches/patch-ab Normal file
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@@ -0,0 +1,25 @@
$NetBSD: patch-ab,v 1.1 2003/10/07 18:20:16 jschauma Exp $
--- delcher.h.orig 2003-10-07 14:07:00.000000000 -0400
+++ delcher.h 2003-10-07 14:07:35.000000000 -0400
@@ -18,9 +18,9 @@
#include <stdio.h>
#include <stdlib.h>
-#include <iostream.h>
-#include <iomanip.h>
-#include <fstream.h>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
#include <math.h>
#include <string.h>
#include <ctype.h>
@@ -31,6 +31,7 @@
#include <errno.h>
#include <unistd.h>
+using namespace std;
#define TRUE 1
#define FALSE 0

15
biology/gnome-chemistry-utils/DESCR Normal file
View File

@@ -0,0 +1,15 @@
GChemPaint, a 2D chemical editor and some other programs related to chemistry
suitable for the GNOME desktop.
The Gnome Chemistry Utils include three utilities:
- a 2D chemical editor (GChemPaint).
- a chemical calculator (computes raw formule, molar weight, mass composition,
etc..) and isotopic pattern).
- a molecule 3d viewer using OpenGL to display molecular models.
- a crystal structues viewer and editor.
- a periodic table of the elements.
- a spectrum viewer.
These programs are based on an included C++ library which provides a few
widgets and various classes, some related to chemistry and some utility
classes.

41
biology/gnome-chemistry-utils/Makefile Normal file
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@@ -0,0 +1,41 @@
# $NetBSD: Makefile,v 1.23 2013/06/06 12:54:06 wiz Exp $
#
DISTNAME= gnome-chemistry-utils-0.12.13
PKGREVISION= 12
CATEGORIES= biology
MASTER_SITES= http://download-mirror.savannah.gnu.org/releases/gchemutils/0.12/
EXTRACT_SUFX= .tar.bz2
MAINTAINER= pkgsrc-users@NetBSD.org
HOMEPAGE= http://gchemutils.nongnu.org/
COMMENT= GChemPaint, a 2D chemical editor and other programs
LICENSE= gnu-gpl-v2 AND gnu-fdl-v1.1
GNU_CONFIGURE= yes
USE_LIBTOOL= yes
USE_TOOLS+= gmake intltool pkg-config msgfmt xgettext msgmerge perl
USE_LANGUAGES= c c++
GCONF_SCHEMAS+= gchemutils.schemas
GCONF_SCHEMAS+= gchempaint-arrows.schemas
GCONF_SCHEMAS+= gcrystal.schemas
GCONF_SCHEMAS+= gchempaint.schemas
BUILDLINK_TRANSFORM+=rm:-DGTK_DISABLE_DEPRECATED
BUILDLINK_TRANSFORM+=rm:-ldl
CONFIGURE_ARGS+= --disable-update-databases
.include "../../devel/GConf/schemas.mk"
.include "../../databases/shared-mime-info/buildlink3.mk"
.include "../../databases/gnome-mime-data/buildlink3.mk"
.include "../../textproc/gnome-doc-utils/buildlink3.mk"
.include "../../mk/omf-scrollkeeper.mk"
.include "../../graphics/gtkglext/buildlink3.mk"
.include "../../misc/goffice0.8/buildlink3.mk"
.include "../../sysutils/desktop-file-utils/desktopdb.mk"
.include "../../biology/chemical-mime-data/buildlink3.mk"
.include "../../biology/bodr/buildlink3.mk"
.include "../../biology/openbabel/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

305
biology/gnome-chemistry-utils/PLIST Normal file
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@@ -0,0 +1,305 @@
@comment $NetBSD: PLIST,v 1.2 2012/07/03 19:32:10 ryoon Exp $
bin/gchem3d
bin/gchem3d-0.12
bin/gchemcalc
bin/gchemcalc-0.12
bin/gchempaint
bin/gchempaint-0.12
bin/gchemtable
bin/gchemtable-0.12
bin/gcrystal
bin/gcrystal-0.12
bin/gspectrum
bin/gspectrum-0.12
lib/gchemutils/0.12/plugins/cdx/cdx.la
lib/gchemutils/0.12/plugins/cdx/plugin.xml
lib/gchemutils/0.12/plugins/cdxml/cdxml.la
lib/gchemutils/0.12/plugins/cdxml/plugin.xml
lib/gchemutils/0.12/plugins/cif/cif.la
lib/gchemutils/0.12/plugins/cif/plugin.xml
lib/gchemutils/0.12/plugins/cml/cml.la
lib/gchemutils/0.12/plugins/cml/plugin.xml
lib/gchemutils/0.12/plugins/paint/arrows.la
lib/gchemutils/0.12/plugins/paint/atoms.la
lib/gchemutils/0.12/plugins/paint/bonds.la
lib/gchemutils/0.12/plugins/paint/cycles.la
lib/gchemutils/0.12/plugins/paint/residues.la
lib/gchemutils/0.12/plugins/paint/selection.la
lib/gchemutils/0.12/plugins/paint/templates.la
lib/gchemutils/0.12/plugins/paint/text.la
lib/gchemutils/0.12/plugins/paint/wikipedia.la
lib/goffice/0.8.17/plugins/gchemutils/gchemutils.la
lib/goffice/0.8.17/plugins/gchemutils/plugin.xml
lib/libgccv-0.12.la
lib/libgcp-0.12.la
lib/libgcu-0.12.la
man/man1/gchem3d.1
man/man1/gchemcalc.1
man/man1/gchempaint.1
man/man1/gchemtable.1
man/man1/gcrystal.1
man/man1/gspectrum.1
share/applications/gchem3d-0.12.desktop
share/applications/gchemcalc-0.12.desktop
share/applications/gchempaint-0.12.desktop
share/applications/gchemtable-0.12.desktop
share/applications/gcrystal-0.12.desktop
share/applications/gspectrum-0.12.desktop
share/gchemutils/0.12/elecprops.xml
share/gchemutils/0.12/elements.xml
share/gchemutils/0.12/isotopes.xml
share/gchemutils/0.12/paint/templates/haworth.xml
share/gchemutils/0.12/paint/templates/templates.xml
share/gchemutils/0.12/paint/themes/ACS_Document_1996
share/gchemutils/0.12/paint/themes/Wikipedia
share/gchemutils/0.12/pixmaps/gchempaint_logo.png
share/gchemutils/0.12/pixmaps/gcrystal_logo.png
share/gchemutils/0.12/radii.xml
share/gchemutils/0.12/residues.xml
share/gchemutils/0.12/space-groups.xml
share/gchemutils/0.12/ui/calc/gchemcalc.ui
share/gchemutils/0.12/ui/crystal/atoms.ui
share/gchemutils/0.12/ui/crystal/bonds.ui
share/gchemutils/0.12/ui/crystal/cell.ui
share/gchemutils/0.12/ui/crystal/cleavages.ui
share/gchemutils/0.12/ui/crystal/docprop.ui
share/gchemutils/0.12/ui/crystal/lines.ui
share/gchemutils/0.12/ui/crystal/prefs.ui
share/gchemutils/0.12/ui/crystal/size.ui
share/gchemutils/0.12/ui/crystal/view-settings.ui
share/gchemutils/0.12/ui/libgcu/gcuperiodic.ui
share/gchemutils/0.12/ui/libgcu/image-resolution.ui
share/gchemutils/0.12/ui/libgcu/image-size.ui
share/gchemutils/0.12/ui/libgcu/print-setup.ui
share/gchemutils/0.12/ui/paint/H-pos.ui
share/gchemutils/0.12/ui/paint/arrow-object.ui
share/gchemutils/0.12/ui/paint/arrow.png
share/gchemutils/0.12/ui/paint/docprop.ui
share/gchemutils/0.12/ui/paint/newfiledlg.ui
share/gchemutils/0.12/ui/paint/plugins/arrows/arrowtool.ui
share/gchemutils/0.12/ui/paint/plugins/arrows/curvedarrowtool.ui
share/gchemutils/0.12/ui/paint/plugins/atoms/orbital-prop.ui
share/gchemutils/0.12/ui/paint/plugins/atoms/orbital.ui
share/gchemutils/0.12/ui/paint/plugins/bonds/bond.ui
share/gchemutils/0.12/ui/paint/plugins/bonds/chain.ui
share/gchemutils/0.12/ui/paint/plugins/cycles/cycle.ui
share/gchemutils/0.12/ui/paint/plugins/cycles/cyclen.ui
share/gchemutils/0.12/ui/paint/plugins/residues/residues.ui
share/gchemutils/0.12/ui/paint/plugins/selection/group.ui
share/gchemutils/0.12/ui/paint/plugins/templates/new-template.ui
share/gchemutils/0.12/ui/paint/plugins/templates/templates.ui
share/gchemutils/0.12/ui/paint/plugins/text/fontsel.ui
share/gchemutils/0.12/ui/paint/preferences.ui
share/gchemutils/0.12/ui/paint/stringdlg.ui
share/gchemutils/0.12/ui/paint/tools.ui
share/gchemutils/0.12/ui/paint/zoom.ui
share/gchemutils/0.12/ui/table/acidity.ui
share/gchemutils/0.12/ui/table/block.ui
share/gchemutils/0.12/ui/table/curve.ui
share/gchemutils/0.12/ui/table/eltpage.ui
share/gchemutils/0.12/ui/table/family.ui
share/gchemutils/0.12/ui/table/state-thermometer.ui
share/gconf/schemas/gchempaint-arrows.schemas
share/gconf/schemas/gchempaint.schemas
share/gconf/schemas/gchemutils.schemas
share/gconf/schemas/gcrystal.schemas
share/glib-2.0/schemas/org.gnome.gchemutils.crystal.gschema.xml
share/glib-2.0/schemas/org.gnome.gchemutils.gschema.xml
share/glib-2.0/schemas/org.gnome.gchemutils.paint.gschema.xml
share/glib-2.0/schemas/org.gnome.gchemutils.paint.plugins.arrows.gschema.xml
share/gnome/help/gchem3d-0.12/C/figures/ball-and-stick.png
share/gnome/help/gchem3d-0.12/C/figures/cylinders.png
share/gnome/help/gchem3d-0.12/C/figures/main-window.png
share/gnome/help/gchem3d-0.12/C/figures/page-setup.png
share/gnome/help/gchem3d-0.12/C/figures/print-scale.png
share/gnome/help/gchem3d-0.12/C/figures/spacefill.png
share/gnome/help/gchem3d-0.12/C/figures/wireframe.png
share/gnome/help/gchem3d-0.12/C/gchem3d-0.12.xml
share/gnome/help/gchem3d-0.12/C/legal.xml
share/gnome/help/gchemcalc-0.12/C/figures/braces.png
share/gnome/help/gchemcalc-0.12/C/figures/composition.png
share/gnome/help/gchemcalc-0.12/C/figures/formula.png
share/gnome/help/gchemcalc-0.12/C/figures/page-setup.png
share/gnome/help/gchemcalc-0.12/C/figures/pattern.png
share/gnome/help/gchemcalc-0.12/C/figures/print-scale.png
share/gnome/help/gchemcalc-0.12/C/figures/start.png
share/gnome/help/gchemcalc-0.12/C/gchemcalc-0.12.xml
share/gnome/help/gchemcalc-0.12/C/legal.xml
share/gnome/help/gchempaint-0.12/C/figures/Hposdlg.png
share/gnome/help/gchempaint-0.12/C/figures/arrow-heads.png
share/gnome/help/gchempaint-0.12/C/figures/arrow-object-dlg.png
share/gnome/help/gchempaint-0.12/C/figures/arrow-object1.png
share/gnome/help/gchempaint-0.12/C/figures/arrow-object2.png
share/gnome/help/gchempaint-0.12/C/figures/arrow-object3.png
share/gnome/help/gchempaint-0.12/C/figures/arrow-opts.png
share/gnome/help/gchempaint-0.12/C/figures/arrows.png
share/gnome/help/gchempaint-0.12/C/figures/bond-opts.png
share/gnome/help/gchempaint-0.12/C/figures/bond.png
share/gnome/help/gchempaint-0.12/C/figures/chain-opt.png
share/gnome/help/gchempaint-0.12/C/figures/chain.png
share/gnome/help/gchempaint-0.12/C/figures/charges.png
share/gnome/help/gchempaint-0.12/C/figures/choose-elt.png
share/gnome/help/gchempaint-0.12/C/figures/curved-arrow-end.png
share/gnome/help/gchempaint-0.12/C/figures/curved-arrow-opts.png
share/gnome/help/gchempaint-0.12/C/figures/curved-arrow.png
share/gnome/help/gchempaint-0.12/C/figures/cycle-opt.png
share/gnome/help/gchempaint-0.12/C/figures/cyclentool-opt.png
share/gnome/help/gchempaint-0.12/C/figures/cyclentool.png
share/gnome/help/gchempaint-0.12/C/figures/cycletools.png
share/gnome/help/gchempaint-0.12/C/figures/delocalized-bond.png
share/gnome/help/gchempaint-0.12/C/figures/downbond.png
share/gnome/help/gchempaint-0.12/C/figures/electrons.png
share/gnome/help/gchempaint-0.12/C/figures/element.png
share/gnome/help/gchempaint-0.12/C/figures/elt-menu.png
share/gnome/help/gchempaint-0.12/C/figures/eraser.png
share/gnome/help/gchempaint-0.12/C/figures/fragment.png
share/gnome/help/gchempaint-0.12/C/figures/ghemical1.png
share/gnome/help/gchempaint-0.12/C/figures/ghemical2.png
share/gnome/help/gchempaint-0.12/C/figures/ghemical3.png
share/gnome/help/gchempaint-0.12/C/figures/group.png
share/gnome/help/gchempaint-0.12/C/figures/main-window.png
share/gnome/help/gchempaint-0.12/C/figures/mechanism-arrows.png
share/gnome/help/gchempaint-0.12/C/figures/merge.png
share/gnome/help/gchempaint-0.12/C/figures/merge1.png
share/gnome/help/gchempaint-0.12/C/figures/merge2.png
share/gnome/help/gchempaint-0.12/C/figures/merge3.png
share/gnome/help/gchempaint-0.12/C/figures/mesomery-arrow.png
share/gnome/help/gchempaint-0.12/C/figures/mesomery1.png
share/gnome/help/gchempaint-0.12/C/figures/mesomery2.png
share/gnome/help/gchempaint-0.12/C/figures/mesomery3.png
share/gnome/help/gchempaint-0.12/C/figures/mol-menu.png
share/gnome/help/gchempaint-0.12/C/figures/new-template.png
share/gnome/help/gchempaint-0.12/C/figures/newfile.png
share/gnome/help/gchempaint-0.12/C/figures/orbital-prop.png
share/gnome/help/gchempaint-0.12/C/figures/orbital-sample.png
share/gnome/help/gchempaint-0.12/C/figures/orbital-toolbox.png
share/gnome/help/gchempaint-0.12/C/figures/orbital.png
share/gnome/help/gchempaint-0.12/C/figures/page-setup.png
share/gnome/help/gchempaint-0.12/C/figures/phenyl-residue.png
share/gnome/help/gchempaint-0.12/C/figures/phenyl-structure.png
share/gnome/help/gchempaint-0.12/C/figures/plus.png
share/gnome/help/gchempaint-0.12/C/figures/preferences.png
share/gnome/help/gchempaint-0.12/C/figures/prefs-arrows.png
share/gnome/help/gchempaint-0.12/C/figures/prefs-atoms-font.png
share/gnome/help/gchempaint-0.12/C/figures/prefs-atoms-other.png
share/gnome/help/gchempaint-0.12/C/figures/prefs-bonds.png
share/gnome/help/gchempaint-0.12/C/figures/prefs-text.png
share/gnome/help/gchempaint-0.12/C/figures/print-scale.png
share/gnome/help/gchempaint-0.12/C/figures/properties.png
share/gnome/help/gchempaint-0.12/C/figures/reaction-arrows.png
share/gnome/help/gchempaint-0.12/C/figures/reaction1.png
share/gnome/help/gchempaint-0.12/C/figures/reaction2.png
share/gnome/help/gchempaint-0.12/C/figures/reaction3.png
share/gnome/help/gchempaint-0.12/C/figures/reaction4.png
share/gnome/help/gchempaint-0.12/C/figures/reaction5.png
share/gnome/help/gchempaint-0.12/C/figures/residues.png
share/gnome/help/gchempaint-0.12/C/figures/retrosynthesis.png
share/gnome/help/gchempaint-0.12/C/figures/retrosynthesis1.png
share/gnome/help/gchempaint-0.12/C/figures/retrosynthesis2.png
share/gnome/help/gchempaint-0.12/C/figures/retrosynthesis3.png
share/gnome/help/gchempaint-0.12/C/figures/retrosynthesis4.png
share/gnome/help/gchempaint-0.12/C/figures/rotate.png
share/gnome/help/gchempaint-0.12/C/figures/selection.png
share/gnome/help/gchempaint-0.12/C/figures/stereobonds.png
share/gnome/help/gchempaint-0.12/C/figures/templates-tools.png
share/gnome/help/gchempaint-0.12/C/figures/templates.png
share/gnome/help/gchempaint-0.12/C/figures/text.png
share/gnome/help/gchempaint-0.12/C/figures/texttools-bar.png
share/gnome/help/gchempaint-0.12/C/figures/toolbox.png
share/gnome/help/gchempaint-0.12/C/figures/wikipedia.png
share/gnome/help/gchempaint-0.12/C/gchempaint-0.12.xml
share/gnome/help/gchempaint-0.12/C/legal.xml
share/gnome/help/gchemtable-0.12/C/figures/add-plot.png
share/gnome/help/gchemtable-0.12/C/figures/atomic-radii.png
share/gnome/help/gchemtable-0.12/C/figures/blocs.png
share/gnome/help/gchemtable-0.12/C/figures/choose-data.png
share/gnome/help/gchemtable-0.12/C/figures/curve.png
share/gnome/help/gchemtable-0.12/C/figures/elec.png
share/gnome/help/gchemtable-0.12/C/figures/electronegativity.png
share/gnome/help/gchemtable-0.12/C/figures/family.png
share/gnome/help/gchemtable-0.12/C/figures/graph-guru.png
share/gnome/help/gchemtable-0.12/C/figures/main.png
share/gnome/help/gchemtable-0.12/C/figures/new-chart-guru.png
share/gnome/help/gchemtable-0.12/C/figures/new-chart.png
share/gnome/help/gchemtable-0.12/C/figures/page-setup.png
share/gnome/help/gchemtable-0.12/C/figures/print-scale.png
share/gnome/help/gchemtable-0.12/C/figures/radii.png
share/gnome/help/gchemtable-0.12/C/figures/start.png
share/gnome/help/gchemtable-0.12/C/figures/state.png
share/gnome/help/gchemtable-0.12/C/figures/thermo.png
share/gnome/help/gchemtable-0.12/C/gchemtable-0.12.xml
share/gnome/help/gchemtable-0.12/C/legal.xml
share/gnome/help/gcrystal-0.12/C/figures/atoms-dlg.png
share/gnome/help/gcrystal-0.12/C/figures/cleavages-dlg.png
share/gnome/help/gcrystal-0.12/C/figures/default-view.png
share/gnome/help/gcrystal-0.12/C/figures/lattice-dlg.png
share/gnome/help/gcrystal-0.12/C/figures/lines-dlg.png
share/gnome/help/gcrystal-0.12/C/figures/main-window.png
share/gnome/help/gcrystal-0.12/C/figures/page-setup.png
share/gnome/help/gcrystal-0.12/C/figures/print-res.png
share/gnome/help/gcrystal-0.12/C/figures/print-scale.png
share/gnome/help/gcrystal-0.12/C/figures/size-dlg.png
share/gnome/help/gcrystal-0.12/C/figures/view-settings.png
share/gnome/help/gcrystal-0.12/C/gcrystal-0.12.xml
share/gnome/help/gcrystal-0.12/C/legal.xml
share/gnome/help/gspectrum-0.12/C/figures/gspectrum.png
share/gnome/help/gspectrum-0.12/C/figures/ir-tools.png
share/gnome/help/gspectrum-0.12/C/figures/nmr-tools.png
share/gnome/help/gspectrum-0.12/C/figures/page-setup.png
share/gnome/help/gspectrum-0.12/C/figures/print-scale.png
share/gnome/help/gspectrum-0.12/C/figures/simple-toolbar.png
share/gnome/help/gspectrum-0.12/C/figures/uv-vis-tools.png
share/gnome/help/gspectrum-0.12/C/gspectrum-0.12.xml
share/gnome/help/gspectrum-0.12/C/legal.xml
share/icons/hicolor/128x128/apps/gchem3d.png
share/icons/hicolor/128x128/apps/gchemcalc.png
share/icons/hicolor/128x128/apps/gchempaint.png
share/icons/hicolor/128x128/apps/gchemtable.png
share/icons/hicolor/128x128/apps/gcrystal.png
share/icons/hicolor/128x128/apps/gspectrum.png
share/icons/hicolor/128x128/mimetypes/application-x-gchempaint.png
share/icons/hicolor/128x128/mimetypes/application-x-gcrystal.png
share/icons/hicolor/32x32/apps/gchem3d.png
share/icons/hicolor/32x32/apps/gchemcalc.png
share/icons/hicolor/32x32/apps/gchempaint.png
share/icons/hicolor/32x32/apps/gchemtable.png
share/icons/hicolor/32x32/apps/gcrystal.png
share/icons/hicolor/32x32/apps/gspectrum.png
share/icons/hicolor/32x32/mimetypes/application-x-gchempaint.png
share/icons/hicolor/32x32/mimetypes/application-x-gcrystal.png
share/icons/hicolor/48x48/apps/gchem3d.png
share/icons/hicolor/48x48/apps/gchemcalc.png
share/icons/hicolor/48x48/apps/gchempaint.png
share/icons/hicolor/48x48/apps/gchemtable.png
share/icons/hicolor/48x48/apps/gcrystal.png
share/icons/hicolor/48x48/apps/gspectrum.png
share/icons/hicolor/48x48/mimetypes/application-x-gchempaint.png
share/icons/hicolor/48x48/mimetypes/application-x-gcrystal.png
share/icons/hicolor/72x72/apps/gchem3d.png
share/icons/hicolor/72x72/apps/gchemcalc.png
share/icons/hicolor/72x72/apps/gchempaint.png
share/icons/hicolor/72x72/apps/gchemtable.png
share/icons/hicolor/72x72/apps/gcrystal.png
share/icons/hicolor/72x72/apps/gspectrum.png
share/icons/hicolor/72x72/mimetypes/application-x-gchempaint.png
share/icons/hicolor/72x72/mimetypes/application-x-gcrystal.png
share/locale/de/LC_MESSAGES/gchemutils-0.12.mo
share/locale/el/LC_MESSAGES/gchemutils-0.12.mo
share/locale/es/LC_MESSAGES/gchemutils-0.12.mo
share/locale/eu/LC_MESSAGES/gchemutils-0.12.mo
share/locale/fr/LC_MESSAGES/gchemutils-0.12.mo
share/locale/it/LC_MESSAGES/gchemutils-0.12.mo
share/locale/pl/LC_MESSAGES/gchemutils-0.12.mo
share/locale/pt_BR/LC_MESSAGES/gchemutils-0.12.mo
share/locale/ru/LC_MESSAGES/gchemutils-0.12.mo
share/locale/zh_CN/LC_MESSAGES/gchemutils-0.12.mo
share/locale/zh_TW/LC_MESSAGES/gchemutils-0.12.mo
share/mime/packages/gchemutils.xml
share/mimelnk/application/x-gchempaint.desktop
share/mimelnk/application/x-gcrystal.desktop
share/omf/gchem3d-0.12/gchem3d-0.12-C.omf
share/omf/gchemcalc-0.12/gchemcalc-0.12-C.omf
share/omf/gchempaint-0.12/gchempaint-0.12-C.omf
share/omf/gchemtable-0.12/gchemtable-0.12-C.omf
share/omf/gcrystal-0.12/gcrystal-0.12-C.omf
share/omf/gspectrum-0.12/gspectrum-0.12-C.omf

8
biology/gnome-chemistry-utils/distinfo Normal file
View File

@@ -0,0 +1,8 @@
$NetBSD: distinfo,v 1.5 2013/05/09 13:45:44 joerg Exp $
SHA1 (gnome-chemistry-utils-0.12.13.tar.bz2) = a3d83f281ccd7fdbc98e14e295093287d8648a69
RMD160 (gnome-chemistry-utils-0.12.13.tar.bz2) = 259509c4e9086fc40e91d1f2f93ad5bad9317b8c
Size (gnome-chemistry-utils-0.12.13.tar.bz2) = 5399998 bytes
SHA1 (patch-libs_gcu_loader-error.h) = 8e223394ac6fb6a17cc23439fc2e3bb2e3bc5440
SHA1 (patch-libs_gcu_spectrumdoc.cc) = 6d4d87c128096006fd384fc058c7942b49df8646
SHA1 (patch-programs_crystal_document.cc) = 192b376922d39796780863720459ee3ef025bfed

12
biology/gnome-chemistry-utils/patches/patch-libs_gcu_loader-error.h Normal file
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@@ -0,0 +1,12 @@
$NetBSD: patch-libs_gcu_loader-error.h,v 1.1 2013/05/09 13:45:45 joerg Exp $
--- libs/gcu/loader-error.h.orig 2013-05-07 20:05:57.000000000 +0000
+++ libs/gcu/loader-error.h
@@ -28,6 +28,7 @@
/*!\file*/
#include <stdexcept>
+#include <string>
namespace gcu {

13
biology/gnome-chemistry-utils/patches/patch-libs_gcu_spectrumdoc.cc Normal file
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@@ -0,0 +1,13 @@
$NetBSD: patch-libs_gcu_spectrumdoc.cc,v 1.1 2013/05/09 13:45:45 joerg Exp $
--- libs/gcu/spectrumdoc.cc.orig 2013-05-07 20:06:58.000000000 +0000
+++ libs/gcu/spectrumdoc.cc
@@ -1618,7 +1618,7 @@ void SpectrumDocument::ReadDataTable (is
break; // this should not occur, but a corrupted or bad file is always possible
s.getline (line, 300);
if (strstr (line, "##")) {
- s.seekg (-strlen (line) -1, _S_cur);
+ s.seekg (-strlen (line) -1, ios::cur);
if (read > npoints) {
g_warning (_("Found too many data!"));
// FIXME: throw an exception

13
biology/gnome-chemistry-utils/patches/patch-programs_crystal_document.cc Normal file
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@@ -0,0 +1,13 @@
$NetBSD: patch-programs_crystal_document.cc,v 1.1 2013/05/09 13:45:45 joerg Exp $
--- programs/crystal/document.cc.orig 2013-05-07 20:13:58.000000000 +0000
+++ programs/crystal/document.cc
@@ -607,7 +607,7 @@ void gcDocument::OnExportVRML (const str
if (error) {
cerr << "gio error: " << error->message << endl;
g_error_free (error);
- g_object_unref (file);
+ g_object_unref (stream);
throw (int) 1;
}
std::map<std::string, sAtom>AtomsMap;

3
biology/gp/DESCR Normal file
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@@ -0,0 +1,3 @@
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.

15
biology/gp/Makefile Normal file
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@@ -0,0 +1,15 @@
# $NetBSD: Makefile,v 1.8 2012/09/11 20:32:12 asau Exp $
#
DISTNAME= gp-0.26
CATEGORIES= biology
MASTER_SITES= http://www.bioinformatics.org/genpak/download/
EXTRACT_SUFX= .tgz
MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://www.bioinformatics.org/genpak/
COMMENT= Manipulate DNA/RNA sequence in a Unix fashion
INSTALLATION_DIRS= bin ${PKGMANDIR}/man1 share/examples
.include "../../mk/bsd.pkg.mk"

49
biology/gp/PLIST Normal file
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@@ -0,0 +1,49 @@
@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
bin/gp_acc
bin/gp_adjust
bin/gp_cdndev
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
man/man1/Genpak.1
man/man1/gp_acc.1
man/man1/gp_adjust.1
man/man1/gp_cdndev.1
man/man1/gp_cusage.1
man/man1/gp_digest.1
man/man1/gp_dimer.1
man/man1/gp_findorf.1
man/man1/gp_gc.1
man/man1/gp_getseq.1
man/man1/gp_matrix.1
man/man1/gp_mkmtx.1
man/man1/gp_pattern.1
man/man1/gp_primer.1
man/man1/gp_qs.1
man/man1/gp_randseq.1
man/man1/gp_seq2prot.1
man/man1/gp_slen.1
man/man1/gp_tm.1
man/man1/gp_trimer.1
share/examples/genpak/ecoli.mtx
share/examples/genpak/enzyme.enz
share/examples/genpak/mporfs.seq
share/examples/genpak/myco.cdn
share/examples/genpak/sample.seq
share/examples/genpak/standard.cdn

7
biology/gp/distinfo Normal file
View File

@@ -0,0 +1,7 @@
$NetBSD: distinfo,v 1.6 2009/09/23 13:34:33 tnn Exp $
SHA1 (gp-0.26.tgz) = 18107463df9bb33d12cc0f0fc6a6f17985492666
RMD160 (gp-0.26.tgz) = 2195e47a09444d7454d3f1314f6b128600fc18ed
Size (gp-0.26.tgz) = 141159 bytes
SHA1 (patch-aa) = bbffa8d814b2974a762f11fea6aed5487bab2cd4
SHA1 (patch-ab) = ce6ec76011f18a9a86b8c65ba5541848e298e27a

121
biology/gp/patches/patch-aa Normal file
View File

@@ -0,0 +1,121 @@
$NetBSD: patch-aa,v 1.5 2009/09/23 13:34:33 tnn Exp $
--- Makefile.orig 2001-05-17 21:27:07.000000000 +0200
+++ Makefile
@@ -5,30 +5,30 @@
######################################################################
# Change the following to suit your needs
-SHELL=/bin/bash
+SHELL=${SH}
# The directory root of your installation
# If you make a personal installation, change it to your home directory
# Default: /usr
# uncomment the following line to install to the default directories...
-TREE=/usr
+TREE=${PREFIX}
# ...or the following line to install into your home directory:
# TREE=$(HOME)
# if you don't have the gd graphic library installed, you have to comment out or
# delete the following line. However, gp_map is such a nice program, so you
# better go to www.boutell.com and download the gd library.
-GDPROGRAMS=gp_map
+# GDPROGRAMS=gp_map
# Directory to install the programs themselves.
# Default: /usr/local/bin
BINDIR=$(TREE)/bin
# directory to install the manual pages
-MANDIR=$(TREE)/man
+MANDIR=$(TREE)/$(PKGMANDIR)
#directory to install the data directory
-DATADIR=$(TREE)/lib
+DATADIR=$(TREE)/share/examples
# documentation.
# If you want to install documents automagically, type:
@@ -67,18 +67,18 @@ clean:
-cd src/ ; rm $(PROGRAMS) core
install: all
- @if [ ! -O "$(BINDIR)" ] ; then \
- echo "File $(BINDIR) doesn't belong to you!" ; exit 1 ; fi
- @cd src ; cp $(PROGRAMS) $(BINDIR)
-
- @if [ ! -O "$(MANDIR)" ] ; then \
- echo "File $(MANDIR) doesn't belong to you!" ; exit 1 ; fi
- @cd man1 ; cp $(MANUALS) $(MANDIR)/man1
-
- @if [ ! -O "$(DATADIR)" ] ; then \
- echo "File $(DATADIR) doesn't belong to you!" ; exit 1 ; fi
- -cd $(DATADIR) ; mkdir genpak ;
- @cd data ; cp -i $(DATAFILES) $(DATADIR)/genpak
+# @if [ ! -O "$(BINDIR)" ] ; then \
+# echo "File $(BINDIR) doesn't belong to you!" ; exit 1 ; fi
+ @cd src ; ${BSD_INSTALL_PROGRAM} $(PROGRAMS) ${DESTDIR}$(BINDIR)
+
+# @if [ ! -O "$(MANDIR)" ] ; then \
+# echo "File $(MANDIR) doesn't belong to you!" ; exit 1 ; fi
+ @cd man1 ; ${BSD_INSTALL_MAN} $(MANUALS) ${DESTDIR}$(MANDIR)/man1
+
+# @if [ ! -O "$(DATADIR)" ] ; then \
+# echo "File $(DATADIR) doesn't belong to you!" ; exit 1 ; fi
+ ${BSD_INSTALL_DATA_DIR} ${DESTDIR}$(DATADIR)/genpak ;
+ @cd data ; ${BSD_INSTALL_DATA} $(DATAFILES) ${DESTDIR}$(DATADIR)/genpak
@echo
@echo Installation is now complete. Type
@@ -99,26 +99,26 @@ filelist:
echo "$(DATADIR)/genpak/"$$i >> FILES.TXT ; done
docs:
- @if [ ! -O "$(TREE)" ] ; \
- then echo "File $(TREE) doesn't belong to you!" ; exit 1 ; fi ; \
- if [ ! -e $(DOCDIR) ] ; \
+# @if [ ! -O "$(TREE)" ] ; \
+# then echo "File $(TREE) doesn't belong to you!" ; exit 1 ; fi ; \
+ if [ ! -d $(DOCDIR) ] ; \
then mkdir $(DOCDIR) ; fi ; \
- if [ ! -e $(DOCDIR)/gp ] ; then \
+ if [ ! -d $(DOCDIR)/gp ] ; then \
mkdir $(DOCDIR)/gp ; fi ; \
cp -r html README.TXT LICENSE.TXT CHANGES.TXT Makefile INSTALL.TXT \
$(DOCDIR)/gp ;
uninstall:
- @if [ ! -O "$(BINDIR)" ] ; \
- then echo "Directory $(BINDIR) doesn't belong to you!" ; \
- exit 1 ; fi
+# @if [ ! -O "$(BINDIR)" ] ; \
+# then echo "Directory $(BINDIR) doesn't belong to you!" ; \
+# exit 1 ; fi
@echo Removing programs...
@cd $(BINDIR) ; rm -f $(PROGRAMS)
- @if [ ! -O "$(MANDIR)" ] ; \
- then echo "Directory $(MANDIR) doesn't belong to you!" ; \
- exit 1 ; fi
+# @if [ ! -O "$(MANDIR)" ] ; \
+# then echo "Directory $(MANDIR) doesn't belong to you!" ; \
+# exit 1 ; fi
@echo Removing manuals...
@cd $(MANDIR)/man1 ; rm -f $(MANUALS)
@@ -127,9 +127,9 @@ uninstall:
@echo Are you sure you really want to remove this data? '(yes/no) '
@read ANSWER ; if [ $ANSWER != "yes" ] ; then \
echo OK, leaving $(DATADIR)/genpak untouched ; else \
- if [ ! -O "$(DATADIR)" ] ; \
- then echo "Directory $(DATADIR) doesn\'t belong to you!" ; \
- exit 1 ; fi ; \
+# if [ ! -O "$(DATADIR)" ] ; \
+# then echo "Directory $(DATADIR) doesn\'t belong to you!" ; \
+# exit 1 ; fi ; \
cd $(DATADIR)/genpak ; rm -f $(DATAFILES) ; fi
-cd $(DATADIR) ; rmdir genpak
@echo

21
biology/gp/patches/patch-ab Normal file
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@@ -0,0 +1,21 @@
$NetBSD: patch-ab,v 1.1.1.1 2003/09/26 03:30:00 jschauma Exp $
--- src/Makefile.orig 2001-05-17 15:27:06.000000000 -0400
+++ src/Makefile 2003-09-25 23:22:01.000000000 -0400
@@ -5,14 +5,13 @@
######################################################################
# Change the following to suit your needs
-SHELL=/bin/bash
-CC=gcc
+SHELL=${SH}
LIBS= -lz -lm
#CFLAGS= -DNLS -DGZ
all: $(PROGRAMS) $(GPPROGRAMS)
-$(PROGRAMS): gp%: gp%.o genpak.h genpak.o
+$(PROGRAMS): gp*: gp*.c genpak.h genpak.o
@echo Creating $@
$(CC) $(CFLAGS) -o $@ genpak.o $< $(LIBS)

10
biology/gromacs/DESCR Normal file
View File

@@ -0,0 +1,10 @@
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins,
lipids and nucleic acids that have a lot of complicated bonded
interactions, but since GROMACS is extremely fast at calculating
the nonbonded interactions (that usually dominate simulations)
many groups are also using it for research on non-biological
systems, e.g. polymers.

42
biology/gromacs/Makefile Normal file
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@@ -0,0 +1,42 @@
# $NetBSD: Makefile,v 1.13 2013/05/31 12:39:39 wiz Exp $
#
DISTNAME= gromacs-4.5.5
PKGREVISION= 3
CATEGORIES= biology
MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/
MAINTAINER= pkgsrc-users@NetBSD.org
HOMEPAGE= http://www.gromacs.org/
COMMENT= Molecular dynamics package
LICENSE= gnu-gpl-v2
# Official recommendation is not to use the gcc 4.1.x set of compilers.
GNU_CONFIGURE= yes
USE_LIBTOOL= yes
USE_PKGLOCALEDIR= yes
USE_TOOLS+= pkg-config
CONFIGURE_ARGS+= --enable-shared
CONFIGURE_ARGS+= --enable-double --program-suffix=
CONFIGURE_ARGS+= --with-gsl
CONFIGURE_ARGS+= --disable-gcc41-check
.include "options.mk"
USE_TOOLS+= perl:run
REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl
CHECK_INTERPRETER_SKIP+= share/gromacs/tutor/gmxdemo/demo
.include "../../mk/bsd.prefs.mk"
.if $(MACHINE_ARCH) == "i386"
CFLAGS+= -msse -msse2
.endif
.include "../../math/fftw/buildlink3.mk"
.include "../../math/gsl/buildlink3.mk" # optional
.include "../../textproc/libxml2/buildlink3.mk" # optional
.include "../../mk/bsd.pkg.mk"

1088
biology/gromacs/PLIST Normal file
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File diff suppressed because it is too large Load Diff

12
biology/gromacs/distinfo Normal file
View File

@@ -0,0 +1,12 @@
$NetBSD: distinfo,v 1.10 2013/04/01 08:00:15 sbd Exp $
SHA1 (gromacs-4.5.5.tar.gz) = ce4b4f9a0453dd2ffea72f28ea0bc7bb7a72f479
RMD160 (gromacs-4.5.5.tar.gz) = a3d40c3ac6ec9ee3e4607bd35afca1dd4715154e
Size (gromacs-4.5.5.tar.gz) = 10398178 bytes
SHA1 (patch-aa) = 60347ad02438d8e13c88c2267030b5793837a419
SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa
SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f
SHA1 (patch-ag) = 810d58d3ad787c9508f775674541775245402596
SHA1 (patch-ah) = 36ceeb409e59d8d3f0abe3bfa3ea3108f61f7a8e
SHA1 (patch-ai) = ed4aa71eb56d1300c67cd17057f72ea452739f3d
SHA1 (patch-aj) = 080d2923d729ff00de0f2cae75a82ec6c3769d6c

28
biology/gromacs/options.mk Normal file
View File

@@ -0,0 +1,28 @@
# $NetBSD: options.mk,v 1.2 2010/05/16 12:04:03 asau Exp $
PKG_OPTIONS_VAR= PKG_OPTIONS.gromacs
PKG_SUPPORTED_OPTIONS+= mpi x11
PKG_SUGGESTED_OPTIONS+= mpi x11
.include "../../mk/bsd.options.mk"
PLIST_VARS= x11
# MPI support:
.if !empty(PKG_OPTIONS:Mmpi)
CONFIGURE_ARGS+= --enable-mpi
PLIST_SUBST+= MPI=_mpi
.include "../../mk/mpi.buildlink3.mk"
.else
PLIST_SUBST+= MPI=
.endif
# X support:
.if !empty(PKG_OPTIONS:Mx11)
CONFIGURE_ARGS+= --with-x
PLIST.x11= yes
.include "../../x11/libX11/buildlink3.mk"
.include "../../x11/libICE/buildlink3.mk"
.include "../../x11/libSM/buildlink3.mk"
.endif

40
biology/gromacs/patches/patch-aa Normal file
View File

@@ -0,0 +1,40 @@
$NetBSD: patch-aa,v 1.3 2013/04/01 08:00:16 sbd Exp $
Allow flags to contain commas.
--- share/template/Makefile.in.orig 2011-09-21 12:38:30.000000000 +0000
+++ share/template/Makefile.in
@@ -250,11 +250,11 @@ XLIBS = -lmd@LIBSUFFIX@ -lgmx@LIBSUFFIX@
XCC = @CC@
@GMX_DOUBLE_FALSE@MYCFLAGS = @CFLAGS@ @INCLUDES@ -I@includedir@
@GMX_DOUBLE_TRUE@MYCFLAGS = @CFLAGS@ @INCLUDES@ -I@includedir@ -DGMX_DOUBLE
-@GMX_DOUBLE_FALSE@template_DATA = template.c README Makefile.@host@ Makefile.pkg
-@GMX_DOUBLE_TRUE@template_DATA = template.c README Makefile.@host@_double Makefile.pkg
+@GMX_DOUBLE_FALSE@template_DATA = template.c README Makefile.@host_alias@ Makefile.pkg
+@GMX_DOUBLE_TRUE@template_DATA = template.c README Makefile.@host_alias@_double Makefile.pkg
EXTRA_DIST = template.c README Template.mak Makefile.pkg CMakeLists.txt.template
BUILT_SOURCES = gromacs
-CLEANFILES = Makefile.@host@ Makefile.@host@_double *~ \\\#*
+CLEANFILES = Makefile.@host_alias@ Makefile.@host_alias@_double *~ \\\#*
template_SOURCES = template.c
LDADD = ../../src/mdlib/libmd@LIBSUFFIX@.la ../../src/gmxlib/libgmx@LIBSUFFIX@.la
all: $(BUILT_SOURCES)
@@ -569,13 +569,13 @@ uninstall-am: uninstall-templateDATA
gromacs:
$(LN_S) $(top_srcdir)/include gromacs
-Makefile.@host@ Makefile.@host@_double: Template.mak Makefile
+Makefile.@host_alias@ Makefile.@host_alias@_double: Template.mak Makefile
cat $(srcdir)/Template.mak | \
- sed 's,@LDFLAGS\@,$(XLDFLAGS),' | \
- sed 's,@LIBS\@,$(XLIBS),' | \
- sed 's,@CFLAGS\@,$(MYCFLAGS),' | \
+ sed 's|@LDFLAGS\@|$(XLDFLAGS)|' | \
+ sed 's|@LIBS\@|$(XLIBS)|' | \
+ sed 's|@CFLAGS\@|$(MYCFLAGS)|' | \
sed 's,@CC\@,$(XCC),' | \
- sed 's,@host\@,@host@,' >$@
+ sed 's,@host\@,@host_alias@,' >$@
#template.$(OBJEXT): gromacs
clean-local:

15
biology/gromacs/patches/patch-ad Normal file
View File

@@ -0,0 +1,15 @@
$NetBSD: patch-ad,v 1.1 2010/05/16 12:04:03 asau Exp $
Libtool wants tag nowadays.
--- src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile.in.orig 2010-05-15 00:44:35.000000000 +0400
+++ src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile.in 2010-05-15 00:49:20.000000000 +0400
@@ -86,7 +86,7 @@
--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCCASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCCASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
SOURCES = $(libnb_kernel_ia32_sse2_la_SOURCES)
DIST_SOURCES = $(libnb_kernel_ia32_sse2_la_SOURCES)

15
biology/gromacs/patches/patch-ae Normal file
View File

@@ -0,0 +1,15 @@
$NetBSD: patch-ae,v 1.1 2010/06/17 09:26:16 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile.in.orig 2009-12-06 21:18:53.000000000 +0000
+++ src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile.in 2010-06-17 07:55:04.000000000 +0000
@@ -86,7 +86,7 @@
--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCCASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCCASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
SOURCES = $(libnb_kernel_ia32_sse_la_SOURCES)
DIST_SOURCES = $(libnb_kernel_ia32_sse_la_SOURCES)

15
biology/gromacs/patches/patch-ag Normal file
View File

@@ -0,0 +1,15 @@
$NetBSD: patch-ag,v 1.2 2010/09/03 20:52:39 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in.orig 2010-07-30 22:55:04.000000000 +0400
+++ src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in 2010-07-31 11:57:35.000000000 +0400
@@ -71,7 +71,7 @@
am__mv = mv -f
CPPASCOMPILE = $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCPPASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCPPASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \

15
biology/gromacs/patches/patch-ah Normal file
View File

@@ -0,0 +1,15 @@
$NetBSD: patch-ah,v 1.2 2010/09/03 20:52:39 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in.orig 2010-07-30 22:55:04.000000000 +0400
+++ src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in 2010-07-31 11:58:30.000000000 +0400
@@ -71,7 +71,7 @@
am__mv = mv -f
CPPASCOMPILE = $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCPPASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCPPASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \

15
biology/gromacs/patches/patch-ai Normal file
View File

@@ -0,0 +1,15 @@
$NetBSD: patch-ai,v 1.1 2010/06/17 09:26:16 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile.in.orig 2009-12-06 21:18:54.000000000 +0000
+++ src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile.in 2010-06-17 07:58:21.000000000 +0000
@@ -86,7 +86,7 @@
--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCCASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCCASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
SOURCES = $(libnb_kernel_x86_64_sse_la_SOURCES)
DIST_SOURCES = $(libnb_kernel_x86_64_sse_la_SOURCES)

15
biology/gromacs/patches/patch-aj Normal file
View File

@@ -0,0 +1,15 @@
$NetBSD: patch-aj,v 1.1 2010/06/17 09:26:16 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile.in.orig 2009-12-06 21:18:54.000000000 +0000
+++ src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile.in 2010-06-17 07:59:09.000000000 +0000
@@ -86,7 +86,7 @@
--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCCASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCCASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
SOURCES = $(libnb_kernel_x86_64_sse2_la_SOURCES)
DIST_SOURCES = $(libnb_kernel_x86_64_sse2_la_SOURCES)

6
biology/hmmer/DESCR Normal file
View File

@@ -0,0 +1,6 @@
HMMER is an implementation of profile HMM methods for sensitive database
searches using multiple sequence alignments as queries. HMMER takes
multiple sequence alignment as input and builds statistical model
called "Hidden Markov Model" which can be used as a query into a
sequence database to find and/or align additional homologues of the
sequence family.

18
biology/hmmer/Makefile Normal file
View File

@@ -0,0 +1,18 @@
# $NetBSD: Makefile,v 1.13 2012/09/11 20:32:12 asau Exp $
#
DISTNAME= hmmer-2.3.2
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GENTOO:=distfiles/}
MAINTAINER= hdp@cs.nmsu.edu
HOMEPAGE= http://hmmer.janelia.org/
COMMENT= Implementation of profile HMM software for protein sequence analysis
PKG_INSTALLATION_TYPES= overwrite pkgviews
GNU_CONFIGURE= yes
MAKE_FLAGS+= MKDIR=${MKDIR:Q}
.include "../../mk/bsd.pkg.mk"

20
biology/hmmer/PLIST Normal file
View File

@@ -0,0 +1,20 @@
@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
bin/hmmalign
bin/hmmbuild
bin/hmmcalibrate
bin/hmmconvert
bin/hmmemit
bin/hmmfetch
bin/hmmindex
bin/hmmpfam
bin/hmmsearch
man/man1/hmmalign.1
man/man1/hmmbuild.1
man/man1/hmmcalibrate.1
man/man1/hmmconvert.1
man/man1/hmmemit.1
man/man1/hmmer.1
man/man1/hmmfetch.1
man/man1/hmmindex.1
man/man1/hmmpfam.1
man/man1/hmmsearch.1

6
biology/hmmer/distinfo Normal file
View File

@@ -0,0 +1,6 @@
$NetBSD: distinfo,v 1.6 2009/07/16 14:53:19 joerg Exp $
SHA1 (hmmer-2.3.2.tar.gz) = aa34cb97cbc43ff3bd92dd111ba5677298fe2d40
RMD160 (hmmer-2.3.2.tar.gz) = 4bf25fc71f332849c76b0a05bca24e88241cee67
Size (hmmer-2.3.2.tar.gz) = 1024933 bytes
SHA1 (patch-aa) = 1d5eae739096ec6398e7cd71b92019d76a677d50

63
biology/hmmer/patches/patch-aa Normal file
View File

@@ -0,0 +1,63 @@
$NetBSD: patch-aa,v 1.4 2009/07/08 15:20:04 joerg Exp $
--- Makefile.in.orig 2003-10-04 21:01:16.000000000 +0200
+++ Makefile.in
@@ -30,11 +30,12 @@ prefix = @prefix@
exec_prefix = @exec_prefix@
BINDIR = @bindir@
MANDIR = @mandir@
+INSTBIN = ${BSD_INSTALL_PROGRAM}
# how to install the man pages;
# cp is generally fine, unless you preformat your pages.
#
-INSTMAN = cp
+INSTMAN = ${BSD_INSTALL_MAN}
MANSUFFIX = 1
# your compiler and compiler flags
@@ -109,13 +110,13 @@ src/libhmmer.a:
# installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
# Creates these directories if they don't exist.
install:
- mkdir -p ${BINDIR}
- -mkdir -p ${MANDIR}/man${MANSUFFIX}
+ ${MKDIR} ${DESTDIR}${BINDIR}
+ -${MKDIR} ${DESTDIR}${MANDIR}/man${MANSUFFIX}
for file in $(PROGS) $(PVMPROGS); do\
- cp src/$$file $(BINDIR)/;\
+ $(INSTBIN) src/$$file ${DESTDIR}$(BINDIR)/;\
done
-for file in hmmer $(PROGS); do\
- $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
done
# uninstall: Reverses the steps of "make install".
@@ -133,7 +134,7 @@ uninstall:
# subdir, remove everything but binaries and Makefiles.
#
bindist:
- mkdir binaries
+ ${MKDIR} binaries
for prog in $(PROGS); do\
(cd binaries; ln -s ../src/$$prog .);\
done
@@ -205,7 +206,7 @@ dist:
# in testsuite.
#
cp ssdk/sqc ${BASENAME}-${RELEASE}/testsuite/
- mkdir ${BASENAME}-${RELEASE}/ssdk
+ ${MKDIR} ${BASENAME}-${RELEASE}/ssdk
cp ssdk/rmanprocess.pl ${BASENAME}-${RELEASE}/ssdk/
#
# Make the configure scripts from configure.ac
@@ -288,7 +289,7 @@ dist:
# directory.
#
ftpdist:
- mkdir -p ${FTPDIR}
+ ${MKDIR} ${FTPDIR}
cp -f hmmer-$(RELEASE)/00README ${FTPDIR}
cp -f hmmer-$(RELEASE)/COPYRIGHT ${FTPDIR}
cp -f hmmer-$(RELEASE)/INSTALL ${FTPDIR}

6
biology/lucy/DESCR Normal file
View File

@@ -0,0 +1,6 @@
A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA
sequence fragments for sequence assembly,possibly using the TIGR
Assembler. The cleanup process includes quality assessment,
confidence reassurance, vector trimming and vector removal. The
primary advantage of Lucy over other similar utilities is that it is a
fully integrated, stand alone program.

30
biology/lucy/Makefile Normal file
View File

@@ -0,0 +1,30 @@
# $NetBSD: Makefile,v 1.8 2012/09/11 20:32:13 asau Exp $
#
DISTNAME= ${PKGNAME:S/-//}
PKGNAME= lucy-1.20
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=lucy/}
MAINTAINER= dprice@cs.nmsu.edu
HOMEPAGE= http://lucy.sourceforge.net/
COMMENT= Sequence Cleanup Program
#LICENSE= LICENSE file say "artistic", but bit differ.
PKG_INSTALLATION_TYPES= overwrite pkgviews
WRKSRC= ${WRKDIR}/${PKGNAME_NOREV}p
AUTO_MKDIRS= yes
PTHREAD_AUTO_VARS= yes
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/lucy ${DESTDIR}${PREFIX}/bin
${INSTALL_MAN} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
cd ${WRKSRC} && ${INSTALL_DATA} PUC19 PUC19splice PUC19splice.for \
PUC19splice.rev atie.seq atie.qul atie.2nd pSPORT1splice \
pSPORT1vector ARMTM40TR.seq ARMTM40TR.qul lucy.ps lucy.debug \
${DESTDIR}${PREFIX}/share/examples/lucy
.include "../../mk/pthread.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

16
biology/lucy/PLIST Normal file
View File

@@ -0,0 +1,16 @@
@comment $NetBSD: PLIST,v 1.3 2009/06/14 17:34:34 joerg Exp $
bin/lucy
man/man1/lucy.1
share/examples/lucy/ARMTM40TR.qul
share/examples/lucy/ARMTM40TR.seq
share/examples/lucy/PUC19
share/examples/lucy/PUC19splice
share/examples/lucy/PUC19splice.for
share/examples/lucy/PUC19splice.rev
share/examples/lucy/atie.2nd
share/examples/lucy/atie.qul
share/examples/lucy/atie.seq
share/examples/lucy/lucy.debug
share/examples/lucy/lucy.ps
share/examples/lucy/pSPORT1splice
share/examples/lucy/pSPORT1vector

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