makeLoChain

This directory contains a suite of scripts
used for generating liftOver chain files and
associated database entries, for use with
the "liftOver" executable, and the "hgLiftOver" CGI.

They are run in the following order:

        makeLoChain-split   kkr1u00
        makeLoChain-align   kk
        makeLoChain-lift    fileserver
        makeLoChain-chain   kk, or kki
        makeLoChain-net     fileserver
        makeLoChain-load    hgwdev
        makeLoChain-cleanup fileserver 

They are run on the KiloKluster, fileserver, or database server --
each script tests that it is being executed on the appropriate
host and gives warning.  Also, each script indicates which
script to run next, and where.

The "split" program creates 10K chunks on /iscratch/i,
which isn't accessible from the pk, so cluster runs
are restricted to kk and kki.

The output file (<old>To<New>.over.chain.gz) is saved to the directory:
    /cluster/data/<old-assembly>/bed/liftOver
It is suggested that commands be executed from this dir,
and output saved there to appropriately named log files.

    Kate
