How to Copy a PGDB Between Computers

This document assumes you know how to copy files or directories in general. If not, please consult your local computer expert.

Each non-built-in PGDB is stored as a directory tree that can be copied from one Pathway Tools installation to another. For example, if the PGDB's Org ID is xyz, its directory tree is ptools-local/pgdbs/user/xyzcyc/ (for Pathway Tools versions 10.0 or older, your PGDB may be found in aic-export/ecocyc/xyzcyc/ or aic-export/pgdbs/biocyc/xyzcyc/ instead, but if you are migrating it to a newer installation, you should place it the new location under the ptools-local directory). Normally, all you have to do is copy that directory tree from one Pathway Tools installation into the corresponding location in another Pathway Tools installation.

Note 1: Once the PGDB is copied to a computer, you have to close and restart the Pathway Tools software on that computer. When Pathway Tools starts up, it will automatically detect the presence of the new PGDB.

Note 2: If the copied PGDB was previously an Oracle or MySQL PGDB (but is now a file PGDB), it is possible that the PGDB may be misconfigured to run as an Oracle or MySQL database. If the PGDB should in fact be accessed in a disk file, ensure that the PGDB type specified in file ptools-local/pgdbs/user/xyzcyc/*/input/organism.dat is FILE. If the PGDB should in fact be accessed from an Oracle or MySQL server, ensure that the PGDB type specified in that file is ORACLE or MYSQL, respectively.

Copying a PGDB from a pre-9.0 version of Pathway Tools to a newer installation

An additional step is required if copying from a Pathway Tools version of 9.0 or older to a Pathway Tools version of 9.5 or newer, for which you should read the following paragraph.

Starting with version 9.5 of Pathway Tools, the use of symbolic links has been replaced by a small file named default-version. You do not have to delete the old symbolic links, but be aware that Pathway Tools 9.5 and newer versions do not use symbolic links. If you copy a PGDB from a Pathway Tools 9.0 or earlier installation to a Pathway Tools 9.5 or later installation, be sure to create a file named default-version in the xyzcyc directory of your Pathway Tools 9.5 or newer installation. For example, if (1) the Org ID is xyz, (2) you've created two versions of it, namely 1.0 and 2.0, and (3) you want 2.0 to be the version that is used by default in the Pathway/Genome Navigator, then the following Unix commands will create the appropriate default-version file:

    cd aic-export/ecocyc/xyzcyc   (for version 9.5)
    cd aic-export/pgdbs/biocyc/xyzcyc  (for version 10.0)
    cd ptools-local/pgdbs/user/xyzcyc  (for version 10.5 or higher)
    echo -n 2.0 > default-version