| blob | 1989a5b021c766766ee80b5ff27737a25dc0fbfe |
1 # $Id: DEPENDENCIES,v 1.4 2006-12-06 18:18:30 sendu Exp $
3 BioPerl Dependencies
5 The following packages are used by BioPerl. Not all are required for
6 BioPerl to operate properly, however some functionality will be missing
7 without them. You can easily choose to install all of these during the
8 normal installation process. Note that the PPM version of the BioPerl
9 packages always tries to install all dependencies.
11 The DBD::mysql, DB_File and XML::Parser modules require other applications
12 or databases: MySQL, Berkeley DB, and expat respectively.
14 NB: This list of packages is not authoritative. See the 'requires',
15 'build_requires' and 'recommends' sections of Build.PL instead.
17 +-----------------------------------------------------------------------------+
18 | Module | Where it is Used | Bio* Modules Affected |
19 |----------------------+-----------------------+------------------------------+
20 | |GenPept | |
21 |HTTP::Request::Common |sequence retrieval, |Bio::DB::* |
22 | |remote http BLAST jobs |Bio::Tools::Run::RemoteBlast |
23 |----------------------+-----------------------+------------------------------|
24 | |GenBank, GenPept | |
25 |LWP::UserAgent |sequence retrieval, |Bio::DB::*, |
26 | |remote http BLAST jobs |Bio::Tools::Run::RemoteBlast |
27 |----------------------+-----------------------+------------------------------|
28 |Ace [1] |Access to AceDB |Bio::DB::Ace |
29 | |databases | |
30 |----------------------+-----------------------+------------------------------|
31 | | |Bio::SeqIO, Bio::Variation::*,|
32 |IO::String |handle to read or |Bio::DB::*, Bio::Index::Blast,|
33 | |write to a string |Bio::Tools::*, Bio::Biblio::IO|
34 | | |Bio::Structure::IO |
35 |----------------------+-----------------------+------------------------------|
36 |XML::Parser [2] |Parsing of XML |Bio::Biblio::IO::medlinexml |
37 | |documents | |
38 |----------------------+-----------------------+------------------------------|
39 |XML::Writer |Parsing + writing of |Bio::SeqIO::game, |
40 | |XML documents |Bio::Variation::* |
41 |----------------------+-----------------------+------------------------------|
42 |XML::Parser::PerlSAX |Parsing of XML |Bio::SeqIO::game, |
43 | |documents |Bio::Variation::*, |
44 | | |Bio::Biblio::IO::medlinexml |
45 |----------------------+-----------------------+------------------------------|
46 | |Parsing of XML |Bio::Variation::IO::xml, |
47 |XML::Twig |documents |Bio::DB::Biblio::eutils, |
48 | | |Bio::Graph::IO::psi_xml |
49 |----------------------+-----------------------+------------------------------|
50 |File::Temp |Temporary File |Bio::DB::FileCache, |
51 | |creation |Bio::DB::XEMBL |
52 |----------------------+-----------------------+------------------------------|
53 |SOAP::Lite |SOAP protocol, |Bio::Biblio::*, |
54 | |XEMBL Services |Bio::DB::XEMBLService |
55 |----------------------+-----------------------+------------------------------|
56 |HTML::Parser |HTML parsing of |Bio::DB::GDB |
57 | |GDB page | |
58 |----------------------+-----------------------+------------------------------|
59 | |MySQL API for loading | |
60 |DBD::mysql [3] |and querying of MySQL- |Bio::DB::GFF, bioperl-db |
61 | |based GFF feature |bioperl-pipeline |
62 | |and BioSQL databases | |
63 |----------------------+-----------------------+------------------------------|
64 |GD [4][5] |GD graphical drawing |Bio::Graphics |
65 | |library | |
66 |----------------------+-----------------------+------------------------------|
67 |Storable |Persistent object |Bio::DB::FileCache |
68 | |storage & retrieval | |
69 |----------------------+-----------------------+------------------------------|
70 |Text::Shellwords |Text parser |Bio::Graphics::FeatureFile |
71 |----------------------+-----------------------+------------------------------|
72 |XML::DOM |XML parser |Bio::SeqIO::bsml, |
73 | | |Bio::SeqIO::interpro |
74 |----------------------+-----------------------+------------------------------|
75 | |Perl access to |Bio::DB::Flat, Bio::DB::Fasta,|
76 |DB_File [6] |Berkeley DB |Bio::SeqFeature::Collection, |
77 | | |Bio::Index::* |
78 |----------------------+-----------------------+------------------------------|
79 |Graph::Directed |Generic graph data and |Bio::Ontology:: |
80 | |algorithms | SimpleOntologyEngine |
81 |----------------------+-----------------------+------------------------------|
82 |Data::Stag:: |Structured Tags, |Bio::SeqIO::chadoitext [7] |
83 | ITextWriter |datastructures | |
84 |----------------------+-----------------------+------------------------------|
85 |Data::Stag:: |Structured Tags, |Bio::SeqIO::chadosxpr [7] |
86 | SxprWriter |datastructures | |
87 |----------------------+-----------------------+------------------------------|
88 |Data::Stag::XMLWriter |Structured Tags, |Bio::SeqIO::chadoxml |
89 | |datastructures | |
90 |----------------------+-----------------------+------------------------------|
91 |Text::Wrap |Very optional |Bio::SearchIO::Writer:: |
92 | | | TextResultWriter |
93 |----------------------+-----------------------+------------------------------|
94 |HTML::Entities |Parse BLAST results in |Bio::SearchIO::blastxml |
95 | |XML | |
96 |----------------------+-----------------------+------------------------------|
97 |Class::AutoClass [8] |Used to create objects |Bio::Graph::SimpleGraph* |
98 |----------------------+-----------------------+------------------------------|
99 |Clone |Used to clone objects |Bio::Graph::ProteinGraph |
100 |----------------------+-----------------------+------------------------------|
101 | | |Bio::SeqIO::bsml_sax, |
102 |XML::SAX |New style SAX parser |Bio::SeqIO::tigrxml, |
103 | | |Bio::SearchIO::blastxml |
104 |----------------------+-----------------------+------------------------------|
105 |XML::SAX::Base |New style SAX parser |Bio::SeqIO::tigrxml |
106 |----------------------+-----------------------+------------------------------|
107 |XML::SAX::Writer | | |
108 |----------------------+-----------------------+------------------------------|
109 |XML::SAX::ExpatXS |New style SAX parser |Bio::SearchIO::blastxml |
110 |[2][9] | | |
111 |----------------------+-----------------------+------------------------------|
112 |XML::Simple [2] |Simple XML parsing |Bio::DB::EUtilities |
113 |----------------------+-----------------------+------------------------------|
114 |Convert::Binary::C |Parsing of DNA strider |Bio::SeqIO::strider |
115 | |documents | |
116 |----------------------+-----------------------+------------------------------|
117 |Spreadsheet:: |Read Microsoft Excel |Bio::SeqIO::excel |
118 | ParseExcel |files | |
119 |----------------------+-----------------------+------------------------------|
120 |Bio::ASN1::EntrezGene |Parses ASN1 format |Bio::SeqIO::entrezgene, |
121 | | |Bio::DB::EntrezGene |
122 +-----------------------------------------------------------------------------+
124 Notes
126 1. Available at http://stein.cshl.org
127 2. Requires expat, at http://sourceforge.net/projects/expat/
128 3. Requires MySQL, from http://www.mysql.org
129 4. Requires GD library (libgd) from http://www.boutell.com/gd
130 5. Installing the GD library - libgd - is somewhat non-trivial since
131 there are a number of dependencies to consider. Matias Giovannini has
132 posted an excellent walkthrough for Mac OS X 10.4.
133 6. Requires Berkeley DB, from Linux RPM or from
134 http://www.sleepycat.com
135 7. These modules may be present in older distributions but are considered
136 redundant; use Bio::SeqIO::chadoxml instead.
137 8. Bio::Graph::SimpleGraph requires Class::AutoClass v. 1.01;
138 earlier versions give very different results.
139 9. This module is optional but recommended for speeding up parsing over
140 the default XML::SAX::PurePerl. If installed, XML::SAX::Expat currently
141 does not work correctly due to DTD problems.