README_pipeline

# Ivana, Nov 2001
# pipeline.pl

# purpose:       Script for running a sequnce of scripts and programs for ET analysis
#                on a list of provided pdb files; each pdbfile should be in its own
#                directory with the same pdb name (this can be done using pdbparser.pl).
#                The idea is to start the whole thing with "ls | pipeline.pl".


# dependencies:  EasyT (--> needs: pretrace, ConvertRawToFasta.pl, 
#                           RetrieveAndClipSequences.pl, blastcl3), 
#                clustalw, TracePlus6.02, ClusterCounterForTrace, ColorProteinByCluster.pl

# assumptions:   All of the dependencies must be reachable through environmental variable $PATH.
#                All of the java classes must be placed in $CLASSPATH directory
#
# godawful solutions: ClusterCounterForTrace is dependent on a huge library currently in
#               Hui's directory - I wasn't successfull in moving it from there
#               (/home/concorde/hy131321/lset/classes )

#  Usage: pipeline.pl [-v e-value] [-s sp] [-e ep] [-d dir] [-n] [-h] 
#  
#    -v          Specify e-value to be used in BLAST. Default: $E_VALUE.
#    -s          Start from the starting point sp in the pipeline.
#    -e          End at the endpoint ep in the pipeline.
#                sp and ep can be one of the following:
#                1 (EasyTrace), 2(clustalw), 3(trace+),
#                4 (ClusterCounter), 5(ColorByCluster),
#                6 (GenerateStatReport).
#    -d          Work in the directory dir.
#    -n          Do not count gap as 21st AA.
#    -h          Print this.