CAMBa Pipeline Installation Information

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Important to Read First
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The following package contains all preprocessing
needed to run the entire mutation detection pipeline
from scratch.  The bioinformatics model described in
the paper is contained within the following script,
which runs on a single gene at a time:

	find_mutations/find_mutations.py

This script depends on a few helper scripts as well as
input from the rest of the pipeline.

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General requirements and installation information:
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1. MAQ - the path in the script files 'maq_*.sh' will
	need to be updated to give the location of
	the MAQ installation.

2. Octave - the path in the script file 'octave_run.sh'
	will need to be updated	to give the location
	of the Octave installation.

3. ClustalW (version 2.0.10)
	- not needed unless there are two or more
	homologs in the run
	- path to executable must be updated in
	'find_mutations/find_mutations.sh'

4. python2.6 (for Scipy)

5. Scipy

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List of Important Scripts:
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scripts/create_scripts.py
scripts/concatenate_all_parsed_pileups.sh
scripts/maq_setup_seqs.sh
scripts/maq_prep.sh
scripts/maq_run.sh
scripts/octave_run.sh
scripts/run_all.sh
scripts/parse_pileup_revised_VVM2.m
scripts/base_change_frequency.py
scripts/get_number_of_reads_for_each_library.sh
scripts/stats.py
scripts/test_for_contamination.py
scripts/get_unique_lines.py
scripts/get_average_frequency_of_each_base_change_from_parsed_pileup.py
scripts/get_average_coverage_by_gene_and_library_from_parsed_pileup.py
scripts/transform_scores_for_bayesian_method_candidates_file.py
scripts/helper_functions.py
scripts/select_top_mutations_from_mutation_candidates_file.py
scripts/process_mutation_candidates_helper_functions.py

find_mutations/select_well_only_mutations_from_mutation_candidates_file.py
find_mutations/get_orphan_statistics_from_mutation_candidates_file.py
find_mutations/generate_find_mutations_file.py
find_mutations/find_mutations.sh
find_mutations/select_sequence_from_file.py
find_mutations/find_mutations.py
find_mutations/homolog_alignment.py
find_mutations/input_output.py
find_mutations/HQ_base_change_frequency.py
find_mutations/clustalw-2.0.10
find_mutations/intermediate_files

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Please report any problems to me at vmissirian@ucdavis.edu
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