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cod-tools -- a set of tools for CIF manipulation.
INSTALLATION
Before the installation of cod-tools, dependencies have to be installed.
Dependency installers for some operating systems are provided with the
cod-tools, under dependencies/, and can be executed as follows:
sh dependencies/Ubuntu-24.04/install.sh
To install cod-tools from a clean distribution, the following steps have
to be executed.
For distributions based on Ubuntu 24.04, the first step should explicitly
specify the non-default version of the GCC compiler due to a bug in the
default version 13.2.0:
# Skip the first step if not on a Ubuntu 24.04-based system
COD_UBUNTU_GCC_MITIGATION="CC=gcc-14 EXTRA_CFLAGS=-fPIC"
make all ${COD_UBUNTU_GCC_MITIGATION}
make check
make install PREFIX=/usr/local/install/cod-tools
Variable 'PREFIX' may be set to any preferred writable location.
ENVIRONMENT SETUP
After a successful installation, several environment variables should
be updated to make the installed programs and libraries automatically
discoverable by the system. This can be done by executing the following
commands:
COD_TOOLS_PREFIX=/usr/local/install/cod-tools
export PATH=${COD_TOOLS_PREFIX}/bin:${PATH}
export PERL5LIB=${COD_TOOLS_PREFIX}/lib/perl5:${PERL5LIB}
export PYTHONPATH=${COD_TOOLS_PREFIX}/usr/local/lib/python${PYTHON_VERSION}/dist-packages:${PYTHONPATH}
Where "${PYTHON_VERSION}" is the Python3 version in the X.Y format
(e.g. '3.10'). On Debian/Ubuntu systems this version can be found by
executing the following command:
py3versions --default --version
For distributions based on Ubuntu 22.04 the PERL5LIB variable should be further
modified to circumvent a bug in the libmath-bigint-gmp-perl software package:
export PERL5LIB=/usr/share/perl/5.34:${PERL5LIB}
The provided commands can also be copied to the ~/.bashrc file to
automatically execute them each time a new shell is started.
BUGS
If you find bugs in cod-tools or have any feedback, please contact us at
cod-bugs@ibt.lt
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