Environment

The Bio-Formats libraries and programs are configured and built to use a set of search paths for different components. It should not be necessary to override these defaults. The bf command will be able to autodetect the installation directory configure paths on most platforms, and the Bio-Formats libraries are also able to determine the paths on most platforms so long as the library search path is configured correctly. However, the following environment variables may be used to override the defaults if this proves necessary:

Installation root

BIOFORMATS_HOME

The root of the installation (if applicable). Setting this will allow the installation to be used in a location other than the one configured. It will also default all the following variables unless they are explicitly overridden individually. This is not useful if an absolute installation path has been configured (e.g. if using /usr/local).

Basic paths

These may be shared with other packages if configured to do so (e.g. if using /usr/local). See GNUInstallDirs for more details. Not all of these paths are currently used, but may be used in the future.

BIOFORMATS_BINDIR

Programs invocable directly by an end user (on the default PATH)

BIOFORMATS_SBINDIR

Programs invocable directly by an end user or admin (not on the default PATH)

BIOFORMATS_SYSLIBEXECDIR

Programs not typically invoked directly (called internally by the Bio-Formats tools and libraries as needed)

BIOFORMATS_SYSCONFDIR

Configuration files

BIOFORMATS_SHAREDSTATEDIR

Shared state

BIOFORMATS_LOCALSTATEDIR

Local state

BIOFORMATS_LIBDIR

Libraries

BIOFORMATS_INCLUDEDIR

C and C++ include files

BIOFORMATS_OLDINCLUDEDIR

C and C++ include files (system)

BIOFORMATS_DATAROOTDIR

Read-only architecture-independent data (root)

BIOFORMATS_SYSDATADIR

Read-only architecture-independent data

BIOFORMATS_INFODIR

GNU Info documentation files

BIOFORMATS_LOCALEDIR

Locale data

BIOFORMATS_MANDIR

Manual pages

BIOFORMATS_DOCDIR

Documentation files

Bio-Formats package-specific paths

These are used only by Bio-Formats and are not shared with other packages. They are all subdirectories under the basic paths, above.

BIOFORMATS_DATADIR

Bio-Formats data files

BIOFORMATS_ICONDIR

Bio-Formats icons

BIOFORMATS_LIBEXECDIR

Bio-Formats program executables

BIOFORMATS_SCHEMADIR

Bio-Formats OME-XML model schemas

BIOFORMATS_TRANSFORMDIR

Bio-Formats OME-XML model transforms