Package: coot Version: 0.6.2.0 Revision: 1 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 , gmp , 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) , imlib , 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) , libtool14 , 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 , gcc44-shlibs (>= 4.4.0-1000) , giflib-shlibs , glib2-shlibs (>= 2.14.0-1) , gmp-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 , imlib-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 , libtool14-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-imlib-prefix=%p --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 -lSystemStubs -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 |include |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 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 << ###############################################################################