Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv17432
Added Files:
clipper.info mmdb.info gpp4.info ssm.info
Log Message:
works for 10.7
--- NEW FILE: gpp4.info ---
Package: gpp4
Version: 1.2.0
Revision: 26
Maintainer: W. G. Scott <[email protected]>
DescPackaging: <<
Based on package created by Morten Kjeldgaard <[email protected]> with minor
edits to conform to standard Fink packaging requirements.
<<
Description: Library providing CCP4 functionality
License: LGPL
GCC:4.0
#Source: http://code.launchpad.net/%n/trunk/%v/+download/gpp4-%v.tar.gz
Source: http://diablo.ucsc.edu/~wgscott/%n/%n-%v.tar.gz
Source-MD5: bb443de0b3385847ea9987f1220e56f1
NoSourceDirectory: false
Depends: %N-shlibs (= %v-%r), gcc46-shlibs
BuildDepends: mmdb-dev (>= 1.23.2-1), ssm-dev (>= 0.1-26), gcc46, pkgconfig
BuildConflicts: g77, fort77, g95
BuildDependsOnly: true
HomePage: http://www.bioxray.dk/~mok/gpp4
DocFiles: README AUTHORS NEWS COPYING
DescDetail: <<
The CCP4 software suite is based around a library of routines that
cover common tasks, such as file opening, parsing keyworded input,
reading and writing of standard data formats, applying symmetry
operations, etc. Programs in the suite call these routines which, as
well as saving the programmer some effort, ensure that the varied
programs in the suite have a similar look-and-feel.
The library contains several subcomponents:
* CMTZ library -- Contains a variety of functions for manipulating
the data structure, for example adding crystals, datasets or columns.
The data structure can be dumped to an output MTZ data file.
* CMAP library -- Functions defining the C-level API for accessing
CCP4 map files.
* CSYM library -- a collection of functions centred around a data file
syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox
of cctbx).
* CCP4 utility library -- many utility functions which either give
specific CCP4 or platform independent functionality.
* CCP4 Parser library -- provides CCP4-style parsing, as used for
processing keywords of CCP4 programs, MTZ header records, etc.
* CCP4 resizable arrays -- defines an object and methods which looks
just like a simple C array, but can be resized at will without
incurring excessive overheads.
<<
CompileScript: <<
#!/bin/bash -evf
LDFLAGS="-L%p/lib/gcc4.4/lib -L%p/lib -L/usr/lib" \
MMDB_CFLAGS="-I%p/include/mmdb" MMDB_LIBS="-L%p/lib" \
FC="gfortran" \
./configure --prefix=%p
make
# CXX="%p/lib/gcc4.4/bin/g++" \
# CC="%p/lib/gcc4.4/bin/gcc" \
<<
InstallScript: <<
make install DESTDIR=%d
<<
SplitOff: <<
Package: %N-shlibs
Files: <<
lib/libgpp4.0.dylib
lib/libgpp4f.0.dylib
<<
Shlibs: <<
%p/lib/libgpp4.0.dylib 1.0.0 %n (>= 1.2.0-1)
%p/lib/libgpp4f.0.dylib 1.0.0 %n (>=1.2.0-1)
<<
<<
SplitOff2: <<
Package: %N-dev
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev, ccp4-dev
Replaces: ccp4-onlylibs-dev, ccp4-dev
Files: <<
lib/*.a
lib/*.la
include/gpp4/ccp4/*.h
share/gpp4/default.def
share/gpp4/environ.def
share/gpp4/syminfo.lib
lib/pkgconfig/*
lib/libgpp4.dylib
lib/libgpp4f.dylib
<<
<<
--- NEW FILE: mmdb.info ---
Package: mmdb
Version: 1.23.2
Revision: 1
Maintainer: W. G. Scott <[email protected]>
DescPackaging: <<
Based on package created by Morten Kjeldgaard <[email protected]> with minor
edits to conform to standard Fink packaging requirements.
<<
Description: Macromolecular coordinate library
License: LGPL
GCC:4.0
HomePage: http://www.ebi.ac.uk/pdbe/docs/cldoc/
Source: http://lmb.bioch.ox.ac.uk/coot/software/dependencies/%n-%v.tar.gz
Source-MD5: c92ef26d6b12ba0930e1d7c20a263987
# build-time stuff in %N-dev, runtime stuff in %N-shlibs, nothing in %N
Depends: fink-obsolete-packages, %n-shlibs (= %v-%r)
BuildDepends: libtool2, automake1.11, autoconf2.6
DescDetail: <<
MMDB is CCP4\'s macromolecular coordinate library, written by Eugene
Krissinel of the EBI. The Coordinate Library is designed to assist
CCP4 developers in working with coordinate files. The major source of
coordinate information remains the PDB files, although more
information becomes available in mmCIF format.
The Library features working with both file formats plus an internal
binary format portable between different platforms. This is achieved
at uniformity of the Library\'s interface functions, so that there is
no difference in handling different formats.
The Library provides various high-level tools for working with
coordinate files, which include not only reading and writing, but also
orthogonal-fractional coordinate transforms, generation of symmetry
mates, editing the molecular structure and some others. The Library is
supposed as a general low-level tool for unifying the
coordinate-related operations.
<<
CompileScript: <<
#!/bin/bash -evf
%p/bin/libtoolize
%p/bin/aclocal
%p/bin/automake --gnu
%p/bin/autoconf
LDFLAGS="-L%p/lib -L/usr/lib" \
./configure --prefix=%p
make
# create missing mmdb.pc
mkdir -p lib/pkgconfig
cd lib/pkgconfig
cat > mmdb.pc << eof
prefix=%p
exec_prefix=\$prefix
libdir=\$prefix/lib
includedir=\$prefix/include
Name: %n
Description: Macromolecular coordinate library
Version: %v
Requires:
Conflicts:
Libs: -L\${libdir} -lmmdb
Cflags: -I\${includedir}
eof
<<
InstallScript: <<
make install DESTDIR=%d
mkdir -p %i/lib/pkgconfig
cp lib/pkgconfig/%n.pc %i/lib/pkgconfig/.
# dpkg requires every package to contain at least one actual file
mkdir -p %i/share/doc/installed-packages
touch %i/share/doc/installed-packages/%n
<<
SplitOff: <<
Package: %N-shlibs
Files: lib/libmmdb.0.dylib
Shlibs: %p/lib/libmmdb.0.dylib 1.0.0 %n (>= 1.12-2)
<<
SplitOff2: <<
Package: %N-dev
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev, ccp4-dev
Replaces: ccp4-onlylibs-dev, ccp4-dev, %N (<< 1.21-13)
Depends: %N-shlibs (= %v-%r)
Files: <<
include/mmdb/*.h
lib/*.a
lib/*.la
lib/pkgconfig/*.pc
lib/libmmdb.dylib
<<
<<
--- NEW FILE: clipper.info ---
Package: clipper
Epoch: 1
Version: 2.1
Revision: 27
GCC:4.0
BuildDepends: <<
fftw (>= 2.1.5-1010) | fftw-mpi (>= 2.1.5-1010),
mmdb-dev (>= 1.23.2-1),
ssm-dev (>= 0.1-26),
gpp4-dev (>= 1.2.0-26),
gcc46
<<
Depends: <<
%n-shlibs (>= %e:%v-%r)
<<
Maintainer: W. G. Scott <[email protected]>
Homepage: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
Source: http://www.ysbl.york.ac.uk/~cowtan/%n/%n-%v-091215-ac.tar.gz
Source-MD5: 003d8c8dd5e3b7bf6b09ef10e9fa31cb
SourceDirectory: %n-%v
DocFiles: README AUTHORS NEWS COPYING
Description: Object-oriented crystallographic libraries
DescDetail: <<
The aim of the project is to produce a set of object-oriented libraries
for the organisation of crystallographic data and the performance of
crystallographic computation. The libraries are designed as a framework
for new crystallographic software, which will allow the full power of
modern programming techniques to be exploited by the developer.
<<
SetCXXFLAGS: -fno-strict-aliasing -I%p/include -I%p/include/mmdb
-I%p/include/ssm -I%p/include/gpp4 -I%p/include/gpp4/ccp4
License: LGPL
CompileScript: <<
#!/bin/bash -evf
# LDFLAGS="-L%p/lib/gcc4.4/lib -L%p/lib -L/usr/lib" \
# CXX="%p/lib/gcc4.4/bin/g++" \
# CC="%p/lib/gcc4.4/bin/gcc" \
LDFLAGS="-L%p/lib -L/usr/lib" \
./configure --prefix=%p --enable-shared --with-gpp4=%p --with-mmdb=%p
--with-fftw=%p --enable-mmdb --enable-minimol --enable-cif --enable-cns
--enable-gpp4
perl -pi -e 's|examples||g' Makefile
# Fix for 10.4 libtool issue
if [[ $(sw_vers -productVersion) < 10.5 ]]; then
sed -e '/verstring=/s/\${wl}//g' < libtool > libtool.fixed
mv libtool.fixed libtool
fi
#
make
<<
InstallScript: <<
make install DESTDIR=%d
<<
SplitOff: <<
Package: %N-shlibs
Depends: <<
fftw-shlibs (>= 2.1.5-1010) | fftw-mpi-shlibs (>= 2.1.5-1010),
mmdb-shlibs (>= 1.23.2-1),
ssm-shlibs (>= 0.1-26),
gpp4-shlibs (>= 1.2.0-26),
gcc46-shlibs
<<
Files: <<
lib/libclipper-ccp4.2.*dylib
lib/libclipper-cif.2.*dylib
lib/libclipper-cns.2.*dylib
lib/libclipper-contrib.2.*dylib
lib/libclipper-core.2.*dylib
lib/libclipper-minimol.2.*dylib
lib/libclipper-mmdb.2.*dylib
lib/libclipper-phs.2.*dylib
<<
Shlibs: <<
%p/lib/libclipper-ccp4.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-cif.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-cns.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-contrib.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-core.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-minimol.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-mmdb.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-phs.2.dylib 3.0.0 %n (>= 1:2.1-1)
<<
<<
SplitOff2: <<
Package: %N-dev
Depends: %N (= %e:%v-%r)
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev, ccp4-dev
Replaces: ccp4-onlylibs-dev, ccp4-dev
Files: <<
lib/*.a
lib/*.la
lib/libclipper-ccp4.dylib
lib/libclipper-cif.dylib
lib/libclipper-cns.dylib
lib/libclipper-contrib.dylib
lib/libclipper-core.dylib
lib/libclipper-minimol.dylib
lib/libclipper-mmdb.dylib
lib/libclipper-phs.dylib
include/*
bin/clipper-config
<<
<<
--- NEW FILE: ssm.info ---
Package: ssm
Version: 0.1
Revision: 26
Maintainer: W. G. Scott <[email protected]>
DescPackaging: <<
Based on package created by Morten Kjeldgaard <[email protected]> with minor
edits to conform to standard Fink packaging requirements. Hack of
ssm_superpose.h
in the install script is required to prevent run-time error in coot.
<<
# Maintainer: Morten Kjeldgaard <[email protected]>
Description: Macromolecular coordinate library
License: LGPL
GCC:4.0
HomePage: http://www.bioxray.dk/~mok/%N
Source: ftp://ftp.bioxray.au.dk/pub/mok/src/%N-%v.tar.gz
Source-MD5: 317d9cc78a88fa5652a4a4b06f329823
NoSourceDirectory: false
Depends: %n-shlibs (= %v-%r)
BuildDepends: mmdb-dev (>= 1.23.2-1)
BuildDependsOnly: true
DocFiles: README AUTHORS NEWS COPYING
DescDetail: <<
SSM is a macromolecular coordinate superposition library, written by
Eugene Krissinel of the EBI.
The library implements the SSM algorithm of protein structure
comparison in three dimensions, which includes an original procedure
of matching graphs built on the protein\'s secondary-structure
elements, followed by an iterative three-dimensional alignment of
protein backbone Calpha atoms.
The algorithm implemented by the software is described in:
E. Krissinel & K. Henrick (2004) Secondary-structure matching (SSM), a
new tool for fast protein structure alignment in three dimensions.
Acta Crystallogr D Biol Crystallogr. 60, 2256-68.
<<
PatchScript: <<
#
# To avoid a conflict with python
#
perl -pi -e 's|FF1|FF1RENAMED|g' src/ssm_superpose.*
perl -pi -e 's|FF2|FF2RENAMED|g' src/ssm_superpose.*
#
<<
CompileScript: <<
#!/bin/bash -evf
# LDFLAGS="-L%p/lib/gcc4.4/lib -L%p/lib -L/usr/lib" \
# CXX="%p/lib/gcc4.4/bin/g++" \
# CC="%p/lib/gcc4.4/bin/gcc" \
LDFLAGS="-L%p/lib -L/usr/lib" \
./configure --prefix=%p
make
<<
InstallScript: <<
make install DESTDIR=%d
<<
SplitOff: <<
Package: %N-shlibs
Files: <<
lib/libssm.0.dylib
lib/libssm.0.0.0.dylib
<<
Shlibs: <<
%p/lib/libssm.0.dylib 1.0.0 %n (>= 0.1-3)
<<
<<
SplitOff2: <<
Package: %N-dev
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev
Replaces: ccp4-onlylibs-dev
Files: <<
lib/*.a
lib/*.la
lib/libssm.dylib
include/ssm/*.h
lib/pkgconfig/ssm.pc
<<
<<
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