programInstaller HOWTO

Mobyle currently allows administrators to publish programs that are either local or imported. The programInstaller script is used to publish them on the server, making them available to the public. This script also handles program indexing.

Overview

Once a Mobyle server has been installed in a MOBYLEHOME directory on the system, the program definitions (i.e., the xml files that describe them to the Mobyle system) are stored in two directories:

  1. the MOBYLEHOME/Programs directory contains program definitions that the administrator has downloaded from distributions,
  2. the MOBYLEHOME/Local/Programs directory contains custom program definitions that have either been created de novo by the server owner, or that he modified to fit his own needs.

In order to publish the programs, the program definitions are copied to a web-accessible directory defined by the server configuration in the DOCUMENT_ROOT/PROGRAMS_URL directory. Therefore, these files will be directly accessible from the Web on the ROOT_URL/PROGRAMS_URL url. This document refers to this directory as www-programs.

The imported program definitions are downloaded via the Web from the www-programs directory of the remote servers. These program definitions are stored in the PROGRAMS_CACHE_PATH directory, which we refer to as www-cache.

The programs index is stored in the MOBYLEHOME/registry_index.json.

Configuration

The configuration of published/imported programs is located in the Local/Config.py file.

The publication of local services is configured by the LOCAL_INSTALL_ORDER, LOCAL_INSTALL_INCLUDE, and LOCAL_INSTALL_EXCLUDE directives. Programs are identified by a list of names that can include jokers.

e.g.:

LOCAL_INSTALL_ORDER=['include' , 'exclude' ]

LOCAL_INSTALL_INCLUDE = [ 'golden', 'clustalw*', 'dnadist', 'fitch', 'kitsch', 'neighbor', 'protdist', 'clique', 'dnapars', 'mix', 'pars', 'protpars', 'consense', 'drawgram', 'drawtree', 'unroot', 'blast2', 'muscle' ]

LOCAL_INSTALL_EXCLUDE=[]

The exportation of services to other portals is defined by the EXPORTED_SERVICES directive, which lists these services.

e.g.:

EXPORTED_SERVICES = [ 'golden', 'abiview' ]

The importation of services from other portals is defined by the PORTALS directive, a dictionary that defines external portals the following way: - the key is the nickname of the portal, as it will appear in the programs list of the portal - for each portal:

  • url is the path to the directory that contains all the cgis (such as job_submit.py).
  • help is the e-mail of the remote portal maintainer, that receives help requests about his job.
  • repository is the path to the directory that contains all the published programs.
  • programs is the list of imported programs.

e.g.:

PORTALS={'portal1': {
          'url': 'http://otherdomain.fr:port/cgi-bin/MobylePortal',
          'help' : 'help@otherdomain.fr',
          'repository': 'http://otherdomain.fr:port/MobyleData/programs',
          'programs': ['clustalw-multialign']
          }
      }

Usage and options

The programInstaller script is located in the $MOBYLEHOME/Tools directory. Before to run it, you should make sure that:

  • your current user has the permissions to read and write the files that belong to the Mobyle user (e.g., apache user).
  • your MOBYLEHOME environment variable is correctly set.

Below are a few examples of how you can use the programInstaller utility. More extensive help can be obtained by typing:

$./programInstaller.py -h