1BP_PAPPLMAKER(1) User Contributed Perl Documentation BP_PAPPLMAKER(1)
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6 papplmaker.PLS - Analysis tools module generator
7
9 # get some help
10 papplmaker.PLS -h
11 # generate module for program 'seqret'
13 papplmaker.PLS -n edit.seqret
14 # ditto, but specify where to find 'seqret'
16 papplmaker.PLS -n edit::seqret
17 -l http://localhost:8080/axis/services
18 # ditto, but specify a non-default access method to 'seqret'
20 papplmaker.PLS -n edit::seqret
21 -l http://corba.ebi.ac.uk/IOR/Analyses.ref
22 -a corba
23 # generate modules for all available analyses
25 # (using default location and default access method)
26 papplmaker.PLS
27 # do not generate but see what would be generated
29 papplmaker.PLS -s
30 papplmaker.PLS -S
31 # generate module for analysis 'edit::seqret'
33 # but name it 'MySeqret'
34 papplmaker.PLS -n edit::seqret -m MySeqret
35 # ...and use it
37 use MySeqret;
38 print new MySeqret->sequence_direct_data ('tatatacccgt')
39 ->osformat ('embl')
40 ->wait_for
41 ->outseq;
42 # ditto but put the result into directory '/tmp/my'
44 # (directories do not need to exist)
45 papplmaker.PLS -n edit::seqret -m MySeqret -d /tmp/my/
46 # generate modules for all analysis whose names
48 # matches given regular expression (case insensitive)
49 papplmaker.PLS -r 'edit'
50 # ditto, but name generated module with your own names
52 # (letting papplmaker.PLS substitute parts of your names)
53 papplmaker.PLS -r 'edit' -m 'My_$ANALYSIS'
54
56 The module "Bio::Tools::Run::Analysis" provides access to the local and
57 remote analysis tools in a unified way (defined in "Bio::AnalysisI").
58 The module uses general approach allowing to set arbitrary input data
59 and to retrieve results by naming them. However, sometimes is more
60 convenient to use a specific module, representing one analysis tool,
61 that already knows about available input and result names.
62 The generator "papplmaker.PLS" creates such dedicated modules.
64 "papplmaker.PLS" uses the same access method as the general module -
66 which means that depending on the parameter "access" it can use SOAP,
67 CORBA or any other (supported) protocol, or it can access local
68 analysis (available on the same machine where "papplmaker.PLS" is
69 invoked).
70 "papplmaker.PLS" does its job either for one named analysis (specified
72 by the "-n" option, or it uses "Bio::Tools::Run::AnalysisFactory"
73 module in order to find what analyses are available, and can limit
74 their number by matching against a regular expression given by the "-r"
75 option.
76 The generated module or modules are named by default similarly to the
78 names of the corresponding analyses, but this can be changed by the
79 "-m" option which is actually a template where the following strings
80 are recognised and replaced:
81 $ANALYSIS or ${ANALYSIS}
83 Will be replaced by the name of the analysis.
84 $CATEGORY or ${CATEGORY}
86 Will be replaced by the name of the category where the analysis
87 belongs to.
88 $SERVICE or ${SERVICE}
90 Will be replaced by the entire name of the service (which is
91 usually a concatenation of a category and a analysis name, and it
92 is used also as a default module name, btw).
93 What is a difference between the "service" and "analysis", and what
95 does "category" mean? Sometimes these terms may be confusing because
96 they may mean slightly different things depending on the access method
97 used to communicate with them. Generally, an "analysis" is a program
98 (an application, a tool) running somewhere, but sometimes on a local
99 machine. An example of an analysis is "seqret" (from the EMBOSS
100 package). The analyses can be grouped into categories by their
101 functions or by type of data they deal with (but sometimes there are no
102 categories at all). Each analyses can be accessed using a higher level
103 of abstraction, a "service". A service is usually a protocol-dependent
104 wrapper, such as a Web Service, or a CORBA service. For example there
105 is a "edit::seqret" service which represents analysis "seqret" in the
106 category "edit".
107
109 Mailing Lists
110 User feedback is an integral part of the evolution of this and other
111 Bioperl modules. Send your comments and suggestions preferably to the
112 Bioperl mailing list. Your participation is much appreciated.
113 bioperl-l@bioperl.org - General discussion
115 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
116 Reporting Bugs
118 Report bugs to the Bioperl bug tracking system to help us keep track of
119 the bugs and their resolution. Bug reports can be submitted via the
120 web:
121 http://bugzilla.open-bio.org/
123
125 Martin Senger (senger@ebi.ac.uk)
126
128 Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.
129 This script is free software; you can redistribute it and/or modify it
131 under the same terms as Perl itself.
132
134 This software is provided "as is" without warranty of any kind.
135
137 None known at the time of writing this.
138perl v5.12.0 2010-04-29 BP_PAPPLMAKER(1)