Import of pkgsrc-2015Q3
This commit is contained in:
@@ -1,4 +1,4 @@
|
||||
# $NetBSD: Makefile,v 1.37 2014/02/20 11:44:51 fhajny Exp $
|
||||
# $NetBSD: Makefile,v 1.38 2015/07/22 19:49:07 asau Exp $
|
||||
#
|
||||
|
||||
COMMENT= Software for the biological sciences
|
||||
@@ -13,6 +13,7 @@ SUBDIR+= clustalw
|
||||
SUBDIR+= coalesce
|
||||
SUBDIR+= fastDNAml
|
||||
SUBDIR+= fluctuate
|
||||
SUBDIR+= gabedit
|
||||
SUBDIR+= genesplicer
|
||||
SUBDIR+= glimmer
|
||||
SUBDIR+= gnome-chemistry-utils
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
# $NetBSD: Makefile,v 1.30 2015/06/12 10:48:25 wiz Exp $
|
||||
# $NetBSD: Makefile,v 1.31 2015/07/12 18:56:07 wiz Exp $
|
||||
|
||||
DISTNAME= BioPerl-1.6.924
|
||||
PKGNAME= ${DISTNAME:tl}
|
||||
@@ -11,7 +11,7 @@ HOMEPAGE= http://www.bioperl.org/
|
||||
COMMENT= Perl tools for computational molecular biology
|
||||
LICENSE= ${PERL5_LICENSE}
|
||||
|
||||
BUILD_DEPENDS+= {perl>=5.19.6,p5-Module-Build>0.42}:../../devel/p5-Module-Build
|
||||
#BUILD_DEPENDS+= {perl>=5.19.6,p5-Module-Build>0.42}:../../devel/p5-Module-Build
|
||||
BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most
|
||||
|
||||
DEPENDS+= p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres
|
||||
@@ -19,10 +19,10 @@ DEPENDS+= p5-Array-Compare-[0-9]*:../../devel/p5-Array-Compare
|
||||
DEPENDS+= p5-Bio-ASN1-EntrezGene-[0-9]*:../../biology/p5-Bio-ASN1-EntrezGene
|
||||
DEPENDS+= p5-Clone-[0-9]*:../../devel/p5-Clone
|
||||
DEPENDS+= p5-Convert-Binary-C-[0-9]*:../../devel/p5-Convert-Binary-C
|
||||
DEPENDS+= {perl>=5,p5-DB_File-[0-9]*}:../../databases/p5-DB_File
|
||||
#DEPENDS+= {perl>=5,p5-DB_File-[0-9]*}:../../databases/p5-DB_File
|
||||
DEPENDS+= p5-Data-Stag>=0.11:../../devel/p5-Data-Stag
|
||||
DEPENDS+= p5-Error-[0-9]*:../../devel/p5-Error
|
||||
DEPENDS+= {perl>=5.10.1,p5-ExtUtils-Manifest>=1.52}:../../devel/p5-ExtUtils-Manifest
|
||||
#DEPENDS+= {perl>=5.10.1,p5-ExtUtils-Manifest>=1.52}:../../devel/p5-ExtUtils-Manifest
|
||||
DEPENDS+= p5-GD-[0-9]*:../../graphics/p5-GD
|
||||
DEPENDS+= p5-Graph>=0.50:../../devel/p5-Graph
|
||||
DEPENDS+= p5-GraphViz-[0-9]*:../../graphics/p5-GraphViz
|
||||
@@ -37,7 +37,7 @@ DEPENDS+= p5-SVG>=2.26:../../graphics/p5-SVG
|
||||
DEPENDS+= p5-Set-Scalar-[0-9]*:../../devel/p5-Set-Scalar
|
||||
DEPENDS+= p5-Sort-Naturally-[0-9]*:../../devel/p5-Sort-Naturally
|
||||
DEPENDS+= p5-Spreadsheet-ParseExcel-[0-9]*:../../math/p5-Spreadsheet-ParseExcel
|
||||
DEPENDS+= {perl>=5.8.1,p5-Storable>=2.05}:../../devel/p5-Storable
|
||||
#DEPENDS+= {perl>=5.8.1,p5-Storable>=2.05}:../../devel/p5-Storable
|
||||
DEPENDS+= p5-XML-Parser-[0-9]*:../../textproc/p5-XML-Parser
|
||||
DEPENDS+= p5-XML-SAX-Writer-[0-9]*:../../textproc/p5-XML-SAX-Writer
|
||||
DEPENDS+= p5-XML-SAX>=0.15:../../textproc/p5-XML-SAX
|
||||
|
||||
40
biology/gabedit/DESCR
Normal file
40
biology/gabedit/DESCR
Normal file
@@ -0,0 +1,40 @@
|
||||
Gabedit is a graphical user interface to computational chemistry
|
||||
packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC,
|
||||
OpenMopac, Orca, PCGamess and Q-Chem.
|
||||
|
||||
It can display a variety of calculation results including
|
||||
support for most major molecular file formats.
|
||||
The advanced "Molecule Builder" allows to rapidly sketch in
|
||||
molecules and examine them in 3D. Graphics can be exported to
|
||||
various formats, including animations.
|
||||
|
||||
Major features
|
||||
|
||||
* Gabedit can create input file for GAMESS(US), GAUSSIAN,
|
||||
MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem.
|
||||
* Gabedit can graphically display a variety of Gamess-US,
|
||||
Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess,
|
||||
Q-Chem, (partially) ErgoSCF and (partially) ADF calculation
|
||||
results, including the following:
|
||||
+ Molecular orbitals.
|
||||
+ Surfaces from the electron density, electrostatic
|
||||
potential, NMR shielding density, and other properties.
|
||||
+ Surfaces may be displayed in solid, translucent and wire
|
||||
mesh modes. they are can be colorcoded by a separate property.
|
||||
+ Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes
|
||||
and the principal axes of the molecule.
|
||||
+ Animation of the normal modes corresponding to vibrational
|
||||
frequencies.
|
||||
+ Animation of the rotation of geometry, surfaces, contours,
|
||||
planes colorcoded, xyz and the principal axes of the molecule.
|
||||
+ Animation of contours, Animation of planes colorcoded.
|
||||
* Gabedit can display UV-Vis, IR and Raman computed spectra.
|
||||
* Gabedit can generate a povray file for geometry (including
|
||||
hydrogen's bond),surfaces (including colorcoded surfaces),
|
||||
contours, planes colorcoded.
|
||||
* Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format.
|
||||
* Gabedit can generate automatically a series of pictures
|
||||
for animation (vibration, geometry convergence, rotation, contours,
|
||||
planes colorcoded).
|
||||
* Simulated Annealing with Molecular Dynamics is implemented in Gabedit
|
||||
(using Amber 99 molecular mechanics parameters).
|
||||
28
biology/gabedit/Makefile
Normal file
28
biology/gabedit/Makefile
Normal file
@@ -0,0 +1,28 @@
|
||||
# $NetBSD: Makefile,v 1.2 2015/07/27 19:47:55 asau Exp $
|
||||
|
||||
PKGNAME= gabedit-2.4.8
|
||||
DISTNAME= GabeditSrc248
|
||||
CATEGORIES= biology
|
||||
MASTER_SITES= $(MASTER_SITE_SOURCEFORGE:=gabedit/)
|
||||
|
||||
MAINTAINER= asau@inbox.ru
|
||||
HOMEPAGE= http://gabedit.sourceforge.net/
|
||||
COMMENT= A Graphical User Interface to computational chemistry packages
|
||||
|
||||
USE_TOOLS= gmake pkg-config
|
||||
|
||||
INSTALLATION_DIRS= bin
|
||||
|
||||
# Skip check for example scripts:
|
||||
CHECK_PORTABILITY_SKIP= utils/Dalton/SGE/submitDalton \
|
||||
utils/Gamess/SGE/submitGamess
|
||||
|
||||
do-configure:
|
||||
cd $(WRKSRC) && cp platforms/CONFIG.unix CONFIG
|
||||
|
||||
do-install:
|
||||
$(INSTALL_PROGRAM) $(WRKSRC)/gabedit $(DESTDIR)$(PREFIX)/bin
|
||||
|
||||
.include "../../x11/gtk2/buildlink3.mk"
|
||||
.include "../../graphics/gtkglext/buildlink3.mk"
|
||||
.include "../../mk/bsd.pkg.mk"
|
||||
2
biology/gabedit/PLIST
Normal file
2
biology/gabedit/PLIST
Normal file
@@ -0,0 +1,2 @@
|
||||
@comment $NetBSD: PLIST,v 1.1.1.1 2015/07/22 19:05:10 asau Exp $
|
||||
bin/gabedit
|
||||
6
biology/gabedit/distinfo
Normal file
6
biology/gabedit/distinfo
Normal file
@@ -0,0 +1,6 @@
|
||||
$NetBSD: distinfo,v 1.1.1.1 2015/07/22 19:05:10 asau Exp $
|
||||
|
||||
SHA1 (GabeditSrc248.tar.gz) = 7a48f42c39258471faa0a3942890c16b6290de41
|
||||
RMD160 (GabeditSrc248.tar.gz) = 8dec36e32d493c8e024b7a5bdc386da48ad79675
|
||||
Size (GabeditSrc248.tar.gz) = 1992373 bytes
|
||||
SHA1 (patch-src_Common_Gabedit.c) = 44d14190db24e88c20618a0167b2699e234288e8
|
||||
14
biology/gabedit/patches/patch-src_Common_Gabedit.c
Normal file
14
biology/gabedit/patches/patch-src_Common_Gabedit.c
Normal file
@@ -0,0 +1,14 @@
|
||||
$NetBSD: patch-src_Common_Gabedit.c,v 1.1.1.1 2015/07/22 19:05:10 asau Exp $
|
||||
|
||||
--- src/Common/Gabedit.c.orig 2013-10-30 12:46:50.000000000 +0000
|
||||
+++ src/Common/Gabedit.c
|
||||
@@ -26,6 +26,9 @@ DEALINGS IN THE SOFTWARE.
|
||||
#include <glib/gi18n.h>
|
||||
#include <stdlib.h>
|
||||
#include <unistd.h>
|
||||
+#if defined(__NetBSD__)
|
||||
+#include <locale.h>
|
||||
+#endif
|
||||
|
||||
#include "Global.h"
|
||||
#include "MenuToolBar.h"
|
||||
Reference in New Issue
Block a user