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Revision: 1.1
Committed: Fri Dec 14 13:54:28 2007 UTC (8 years, 6 months ago) by gawi79
Branch: MAIN
CVS Tags: HEAD
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1 #####################################################
2 # YAMAP - Yet Another Metagenomic Annotation Pipeline
3 #####################################################
4
5 Gareth Wilson, 2007
6
7 YAMAP, originally developed by Dr. Milo Thurston, is a Perl application created for the NERC Microbial Metagenomics programme (http://www.genomics.ceh.ac.uk/mm/). It utilises Perl TK to provide a graphical interface to the user. YAMAP is designed to allow users to run a selection of first pass annotation tools on their sequence data. Examples of these tools include Glimmer and tRNAscan. The application is available to Bio-linux users.
8
9 To run YAMAP, simply type yamap on the command line, this will load up the graphical interface.
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11 Help on the individual components can be obtained through the graphical interface.
12
13 #########################
14 # YAMAP's Scripts
15 #########################
16
17 yamap.pl - This script contains the code for generating the YAMAP GUI. Actions performed by the user will alter the value of variables in the relevant configuration (.ini) file.
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19 yamap_nogui.pl - This script obtains values from the .ini files. These values are used to determine the executables to be launched from within this script and also the parameters to be used in the executables.
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21 quickmine.pl - Co-ordinates the quickmine pipeline. Obtains variables from quickmine.ini and launches the necessary executables. The scripts that makes up the QuickMine pipeline are listed below.
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23 *_parse_artemis.pl - Each external program that is used in YAMAP will generate output in different formats. Therefore there is a parser script for each, this formats the output ready to be used in artemis. The files produced are .tab files.
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25 yamap_embl.pl - This obtains the various output .tab files and merges them to create a single embl file for input into artemis.
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27 run_art.pl - launches artemis.
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29
30
31 ##############################
32 # YAMAP's Configuration Files
33 ##############################
34
35 The three config files are found in the .yamap directory in the users home directory. If they're not present, they will be automatically generated when YAMAP launches.
36
37 yamap_paths.ini - contains the paths to the different executables (both processing and parsing). Also contains the YAMAP version as a variable. If this doesn't match the current version of YAMAP, the user will be warned that their config file is out of date.
38
39 yamap_run.ini - contains variables determining whether or not a particular program is executed. Also contains variables representing parameters for each executable.
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41 quickmine.ini - contains all the parameters required to run quickmine. This includes paths to input/output, variables indicating which parts of the pipeline should be run, endings for the filenames and parameters for the executables.
42
43
44 ###############################
45 # QuickMine Scripts
46 ###############################
47
48 QuickMine consists of a number of perl scripts, each of which generates different output file types. The order in which they are processed is as follows:
49
50 2qmfasta.pl
51 fasta_html.pl
52 formatdb (executable to create blast database)
53 BLAST
54 quick_splitblast.pl
55 get_orphans.pl
56 hitsparser.pl
57 genetable.pl
58 orphan_count.pl
59 orphan_size.pl
60 paralogue_count.pl
61 incremental_orphan.pl
62 orphan_time.pl
63 binary_matrix.pl
64 #the following need gnuplot to be installed
65 gnu_plotter.pl
66 gnu_percent_plotter.pl
67 genome_plot.pl
68 genome_percent_plot.pl
69 dot_plot.pl
70 #
71 summarizer.pl
72
73
74
75 #################################
76 # Old Files
77 #################################
78
79 It appears some files were unnecessarily included in the last package. These are artifacts of development and are no longer needed. They include:
80 yamap_gui.pl
81 blasttoxls.pl
82 crunchtoxls.pl