Difference between revisions of "Bioscape Dependencies"

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(Moved note to a separate page. Removed Lucene from the dependencies.)
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{{:Bioscape Status}}
'''Please note that this documentation covers an unreleased product and is for internal use only.'''
== Dependencies ==
== Dependencies ==
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For <tt>bsindex</tt>:
For <tt>bsindex</tt>:
* PyLucene (the Lucene text indexing solution) or...
* Xapian core plus bindings (text indexing)
* Xapian core plus bindings (text indexing)
* <tt>bsadmin</tt> (the Bioscape administrative application)
* <tt>bsadmin</tt> (the Bioscape administrative application)

Latest revision as of 13:37, 14 July 2010

NoteNotePlease note that this documentation covers an unreleased product and is for internal use only.


Bioscape has the following basic dependencies.

For bsadmin:

  • PostgreSQL (a relational database system)
  • pyPgSQL (access to PostgreSQL from Python)
  • egenix-mx-base (required by pyPgSQL)
  • sqlliterals (tokenisation of SQL)
  • cmdsyntax (command option processing)
  • NCBI Tools (ASN.1 file parsing, optional)

For bsindex:

  • Xapian core plus bindings (text indexing)
  • bsadmin (the Bioscape administrative application)
  • cmdsyntax (command option processing)
  • pprocess (for use of multiple processes)

For bsweb:

  • bsindex (the Bioscape text indexing application) plus dependencies
  • bsadmin (the Bioscape administrative application) plus dependencies
  • WebStack plus dependencies
  • XSLTools plus dependencies
  • libxml2dom plus dependencies
  • cmdsyntax (command option processing)
  • Apache (or equivalent Web server)

Scripts providing guidance for downloading and building these dependencies are provided in the docs/dependencies directory of the bsadmin distribution.

Additional Resources

Some additional resources have been bundled with the software. See the README.txt files in the distributions for more information.

External Resources

Bioscape makes extensive use of data provided by Entrez Gene and PubMed, as well as Entrez Taxonomy, ChEBI and Gene Ontology.