Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv29944
Added Files:
coot.info
Log Message:
minor changes in dependencies to make this work for 10.7
--- NEW FILE: coot.info ---
Package: coot
Version: 0.6.2.0
Revision: 3
SourceDirectory: %n-0.6.2
#SourceDirectory: %n-%v
GCC: 4.0
Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
# Source:
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-3%r.tar.gz
Source-MD5: 832c4c2216974095bc2298b30108bec4
Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac_dictionary.tar.gz
Source2-MD5: d6eab829728608d0b8eade38debcedd3
Source3:
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
Source3-MD5: 257ab90d44f1c877ada96720dbb87c13
###############################################################################
Description: Crystallographic molecular graphics
DescDetail: <<
Coot stands for Crystallograhic Object Oriented Toolkit. It is a toolkit and
interactive molecular graphical display and manipulation program designed for
macromolecular crystallography. Coot uses professional (and free) widgets (with
the gui builder glade), mmdb, clipper, and OpenGL, together with a new approach
to map contouring and importing/creation and other (modelling) operations. The
mmdb, clipper, ssm and mccp4 libraries are provided in individual fink packages
that replace the now obsolete ccp4-onlylibs-dev fink package. On-line
documentation is available from the coot website accessed via the help menu,
or manually, via the web-site, (see below) and is updated regularly.
.
To have an Aqua-like Coot gtk+2 environment, issue the following command:
echo "include \"%p/share/themes/Glossy_P/gtk-2.0/gtkrc\"">~/.gtkrc-2.0
or simply create a file called ~/.gtkrc-2.0 and put this line in it:
include \"%p/share/themes/Glossy_P/gtk-2.0/gtkrc\"
.
Install povray and raster3d fink packages to use the F8 key for producing
ray-traced images. You may have to re-map the Spaces.app keybinding.
.
Coot now works with Zalman LCD hardware stereo and old-fashioned CRT hardware
stereo on OS X.
<<
###############################################################################
Recommends: povray, ccp4, raster3d
BuildDepends: <<
fink (>= 0.24.12) ,
clipper-dev (>= 1:2.1-26) ,
gpp4-dev (>= 1.2.0-26) ,
mmdb-dev (>= 1.23.2-1) ,
ssm-dev (>= 0.1-26) ,
atk1 (>= 1.20.0-1) ,
cairo (>= 1.6-1) ,
expat1 ,
fftw | fftw-mpi ,
fontconfig2-dev (>= 2.4.1-1) ,
freetype219 (>= 2.3.5-1) ,
freeglut ,
giflib ,
glib2-dev (>= 2.14.0-1) ,
glitz ,
gmp5 ,
gsl ,
gtk+2 (>= 2.12.0-1) ,
gtk+2-dev (>= 2.12.0-1) ,
gtkglext1 ,
guile18 ,
guile18-dev ,
guile18-lib ,
guile18-gtk-dev (>= 2.0-10) ,
libart2 (>= 2.3.16-2) ,
libcurl4 ,
libgettext3-dev ,
libglade2 (>= 2.6.2-1) ,
libgnomecanvas2-dev (>= 2.20.0) ,
libiconv-dev ,
libjpeg8 ,
libpng3 ,
librsvg2-gtk (>= 2.20.0-1) ,
libtool2 ,
libxml2 ,
pango1-xft2-ft219-dev (>= 1.18.4-1) ,
pixman (>= 0.10.0-1) ,
pygtk2-gtk-py27-dev ,
pygobject2-py27-dev ,
python27 ,
swig ,
x11-dev ,
xft2-dev
<<
#
Depends: <<
clipper-shlibs (>= 1:2.1-26) ,
gpp4-shlibs (>= 1.2.0-26) ,
mmdb-shlibs (>= 1.23.2-1) ,
ssm-shlibs (>= 0.1-26) ,
atk1-shlibs (>= 1.20.0-1) ,
coot-shlibs (= %v-%r) ,
fftw-shlibs | fftw-mpi-shlibs ,
freeglut-shlibs ,
gcc46-shlibs ,
giflib-shlibs ,
glib2-shlibs (>= 2.14.0-1) ,
gmp5-shlibs ,
gnome-themes-glossy-p ,
gsl-shlibs ,
gtk+2-shlibs (>= 2.12.0-1) ,
gtkglext1-shlibs ,
guile18 ,
guile18-gtk (>= 2.0-9) ,
guile18-gtk-shlibs (>= 2.0-9) ,
guile18-gui ,
guile18-lib ,
guile18-shlibs ,
libart2-shlibs ,
libcurl4-shlibs ,
libgettext3-shlibs ,
libgnomecanvas2-shlibs (>= 2.20.0),
libiconv ,
libjpeg8-shlibs ,
libpng3-shlibs ,
librsvg2-shlibs (>= 2.20.0-1) ,
libtiff-shlibs ,
libtool2-shlibs ,
librsvg2-gtk (>= 2.20.0-1) ,
libxml2-shlibs ,
pango1-xft2-ft219-shlibs (>= 1.18.4-1) ,
pygtk2-gtk-py27 ,
python27 ,
x11
<<
#
###############################################################################
BuildDependsOnly: false
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchFile: %n.patch
PatchFile-MD5: 847c69ea1ded1d4238b66ab4840a8141
PatchScript: <<
sed 's|@PREFIX@|%p|g' <%{PatchFile} | patch -p1
perl -pi -e 's|ccp4c=ccp4c|ccp4c=gpp4|g' configure
<<
###############################################################################
ConfigureParams: <<
--with-gpp4=%p --with-mmdb=%p --with-ssmlib-prefix=%p --with-clipper-prefix=%p
\
--with-fftw=%p --with-gnomecanvas-prefix=%p --with-gtk2 --with-glut-prefix=%p
\
--with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
\
--with-gtkgl-prefix=%p --with-glib-prefix=%p \
--with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p
<<
###############################################################################
CompileScript: <<
#!/bin/bash -efv
alias python=%p/bin/python2.7
export PYTHON=%p/bin/python2.7
export python=%p/bin/python2.7
export GUILE=%p/bin/guile-1.8
if [[ $(sw_vers -productVersion) < 10.6 ]]; then
export PATH=%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH
else
export
PATH=%p/var/lib/fink/path-prefix-10.6:%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH
fi
export SED=/usr/bin/sed
export GDK_USE_XFT='1'
export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
export
PKG_CONFIG_PATH=%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:%p/lib/pkgconfig:${PKG_CONFIG_PATH}
FLIBS="-L%p/lib" \
CPPFLAGS="-I%p/include/libglade-2.0/glade -I%p/include/libglade-2.0
-I%p/include/python2.7 -I%p/include/mmdb -I%p/include/ssm
-I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include -I/usr/X11R6/include" \
LDFLAGS="-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
-L%p/lib/pango-ft219/lib -L%p/lib -L/usr/lib -flat_namespace
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \
DYLD_LIBRARY_PATH="" \
./configure %c
#
# Force coot to link to single-precision fftw libraries. The double-precision
libraries
# cause coot to crash.
find . -name "Makefile" -exec perl -pi -e 's|lrfftw |lsrfftw |g' '{}' \;
find . -name "Makefile" -exec perl -pi -e 's|lfftw |lsfftw |g' '{}' \;
perl -pi -e 's|include <rfftw.h>|include <srfftw.h>|g'
surface/CXXFFTSolventMap.h
#
if [[ $(sw_vers -productVersion) < 10.5 ]]; then
# Fix libtool compatibility issues
sed -e '/verstring=/s/\${wl}//g' < libtool > libtool.fixed
mv libtool.fixed libtool
fi
#
NUMPROC="$(sysctl -n hw.ncpu)"
make -j $NUMPROC
<<
###############################################################################
InstallScript: <<
#!/bin/zsh -efv
export PATH=$PWD/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
export SED=/usr/bin/sed
export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
#cp src/coot.py python/coot.py
#
NUMPROC="$(sysctl -n hw.ncpu)"
make -j $NUMPROC install prefix=%i
#
# Clean up the 120 MB mess, which zsh makes so much fun:
/bin/rm -f **/*.o
# Add ancillary files to %i/share/coot:
#
mkdir -p %i/share/coot/etc
mkdir -p %i/share/coot/python
mkdir -p %i/bin
# cp src/coot.py %i/share/coot/python/coot.py
# This installs the refmac monomer library
mkdir -p %i/share/coot/lib/data
cp -R ../dic %i/share/coot/lib/data/monomers
cp %i/share/coot/lib/data/monomers/ener_lib.cif %i/share/coot/lib/.
# Reference structures should be in %i/share/coot/reference-structures
cp -R ../reference-structures %i/share/coot/.
cp -R * %i/share/coot/etc/.
# The original wrapper creates problems. Get rid of it.
# Replace with a new wrapper to set the required PYTHONPATH variable
# and a few others as follows:
/bin/rm -f %i/bin/coot
echo '#!/bin/sh -f ' > %i/bin/coot
echo "export COOT_REFMAC_LIB_DIR=%p/share/coot/lib" >> %i/bin/coot
echo "export COOT_PYTHON_DIR=%p/share/coot/python" >> %i/bin/coot
echo 'export COOT_SBASE_DIR="$CCP4/share/sbase"' >> %i/bin/coot
echo "export
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH"
>> %i/bin/coot
#echo "export
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5:%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH"
>> %i/bin/coot
echo "%p/bin/coot-real \"\$@\" " >> %i/bin/coot
chmod a+x %i/bin/coot
# Clean up the rest of the mess.
/bin/rm -rf %i/include %i/**/.libs %i/lib/*.la %i/share/coot/etc/**/*.la
<<
###############################################################################
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
License: GPL
Maintainer: W. G. Scott <[email protected]>
Homepage: http://lmb.bioch.ox.ac.uk/coot
###############################################################################
#
SplitOff: <<
Package: %N-shlibs
Files: <<
lib/libccp4mg-*.0*.dylib
lib/libcoot-*.0*.dylib
lib/libcootaneer.0*.dylib
<<
Shlibs: <<
%p/lib/libccp4mg-surface.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libccp4mg-utils.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-AngleInfo.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-cabuild.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-compat.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-coord-utils.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-coords.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-db-main.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-ideal.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-isosurface.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-lidia-core.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-ligand.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-map-heavy.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-map-utils.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-shelx.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-surface.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-tw.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcoot-utils.0.dylib 1.0.0 %n (>= 0.6-1)
%p/lib/libcootaneer.0.dylib 1.0.0 %n (>= 0.6-1)
<<
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
<<
#
###############################################################################
#
SplitOff2: <<
Package: %N-dev
Depends: %N (= %v-%r)
BuildDependsOnly: True
Files: <<
lib/*.a
<<
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
<<
###############################################################################
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