Configuring METAREP

jcvi edited this page Sep 14, 2010 · 29 revisions

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You can configure METAREP by editing the METAREP configuration file which is located in <installation-dir>/METAREP/app/conf/metarep.php. The following describes the variables that can be defined:

Point this variable to your Apache METAREP webroot directory
Default: /<your-installation-dir>/apache-2.2.14/htdocs/metarep

Directory to store temporary files. Temporary files include CAKEPHP cache/application and R files
Default: /tmp

Solr instance directory. Contains Solr configuration files in conf/ subdirectory
Default: /your-installation-dir>/apache-solr-1.4.0/metarep-solr/

Defines location of Solr index files
Default: /<your-installation-dir>/apache-solr-1.4.0/metarep-solr/data/

Defines Solr port

Solr master server host. Takes on role of master in load balanced/replication set up.
Default: localhost

Define the Solr slave host if you use METAREP in a load balanced/replication set up

Define Solr BIG-IP if you use METAREP in a load balanced/replication set up

Email is displayed if METAREP can not access the Solr or MySQL servers. It is also used to provide users an Email address send bug reports and feature requests.

METAREP distinguishes between four types of users: ADMIN, INTERNAL, EXTERNAL, and PUBLIC. ADMIN and INTERNAL users can access all METAREP datasets, while EXTERNAL and PUBLIC have restricted access. The variable defines the Email extension that is used to identify INTERNAL users. This is especially helpful if you like to grant access to all users of your institution – just specify your institute’s email extension.

The METAREP search and browse pages summarize annotation data types in the form of
sorted top ten lists. Change this variable to increase/decrease the number of top hits shown
for each data type.
Default: 10

The METAREP search page displays pages of found annotation results. By default, ten hits are shown per page.
Change this variable to increase/decrease the number of results that are shown for each result page.
Default: 10

Define the path to your Rscript executable
Default: /usr/local/bin/Rscript

Define the path to your R executable
Default: /usr/local/bin/R

Setting this variable to 1, activates JCVI-only features that access JCVI resources that are not included in this distribution.
Default: 0