How to install in a directory

Note that directory INSTALLDIR must exist.

Run:

./install.sh -d INSTALLDIR

You may have to set some environment variables in order to use bii_scripts at that location. See 'Configuring your environment' below.

How to install in a Python virtual environment

Note that directory INSTALLDIR must exist.

Run:

./install.sh -c config-pyenv -d INSTALLDIR

All python programs and libraries should be found if you have activated your Python virtual environment with source INSTALLDIR/bin/activate. However, for the Perl libraries you still have to set the PERL5LIB environment variable. See 'Configuring your environment' below.

How to install at PYTHONUSERBASE

If you have defined environment variable PYTHONUSERBASE and the directory defined in this variable exists, you can install bii_scripts there with this command:

./install.sh -c config-pyenv -d $PYTHONUSERBASE

If you have set up your environment for PYTHONUSERBASE, all python programs and libraries should be found. However, for the Perl libraries you still have to set the PERL5LIB environment variable. See 'Configuring your environment' below.

How to install on a HZB host

Note: 'HZB' means 'Helmholtz Zentrum Berlin'.

Note: ./install.sh -h lists all HZB hosts, for which a specialized configuration file exists. For these hosts simply run:

./install.sh

On these hosts all environment variables for using bii_scripts should already be configured so you can skip 'Configuring your environment' below.

Finding the scripts: PATH

In order for the scripts of bii_scripts to be found by your shell you may have to set the PATH environment variable.

Try this command:

bii_scripts-env.sh -h

If the command is not found, you have to set your PATH variable. This command shows how PATH must be set (you must know 'INSTALLDIR', the directory where you installed bii_scripts:

INSTALLDIR/bin/bii_scripts-env.sh --path

You may want to add this line to your shell configuration. For bash this is file $HOME/.bashrc.

Finding Python libraries: PYTHONPATH

Try this command:

python3 -c 'import bii_scripts3'

If this cannot find bii_scripts3, you should set the PYTHONPATH variable.

The following command shows how PYTHONPATH should be set:

bii_scripts-env.sh --pythonpath

Finding Perl libraries: PERL5LIB

Try this command:

perl -e 'use canlink'

If this cannot find the 'canlink' module, you should set the PERL5LIB variable.

The following command shows how PERL5LIB should be set:

bii_scripts-env.sh --perl5lib