1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/b5ea0e100bda/ Changeset: b5ea0e100bda User: inithello Date: 2013-05-03 21:55:56 Summary: Rename install_repository_tools to install_tool_shed_repositories. Use shed_util_common.url_join to generate the API url. Affected #: 1 file

diff -r 75e7383c5c794e02503dc03e0d5daf3694323b7d -r b5ea0e100bdaf47d53d11fa2beb39f4218fa8136 scripts/api/install_tool_shed_repositories.py --- /dev/null +++ b/scripts/api/install_tool_shed_repositories.py @@ -0,0 +1,52 @@ +#!/usr/bin/env python +""" +Install a specified repository revision from a specified tool shed into Galaxy. This example demonstrates installation of a repository that contains +valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section. +You can choose if tool dependencies or repository dependencies should be installed, use --repository-deps or --tool-deps. + +This example requires a tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain a tool panel section like the following: + +<section id="from_test_tool_shed" name="From Test Tool Shed" version=""> +</section> + +Here is a working example of how to use this script to install a repository from the test tool shed. +./install_repository_tools.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb --tool-deps +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit + +def main( options ): + """Collect all user data and install the tools via the Galaxy API.""" + data = {} + data[ 'tool_shed_url' ] = options.tool_shed_url + data[ 'name' ] = options.name + data[ 'owner' ] = options.owner + data[ 'changeset_revision' ] = options.changeset_revision + if options.tool_panel_section_id: + data[ 'tool_panel_section_id' ] = options.tool_panel_section_id + elif options.new_tool_panel_section_label: + data[ 'new_tool_panel_section_label' ] = options.new_tool_panel_section_label + if options.install_repository_dependencies: + data[ 'install_repository_dependencies' ] = options.install_repository_dependencies + if options.install_tool_dependencies: + data[ 'install_tool_dependencies' ] = options.install_tool_dependencies + submit( options.api, '%s%s' % ( options.local_url.strip('/'), '/api/tool_shed_repositories/new/install_repository_revision' ), data ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) + parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" ) + parser.add_argument( "-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance." ) + parser.add_argument( "-n", "--name", required=True, help="Repository name." ) + parser.add_argument( "-o", "--owner", required=True, help="Repository owner." ) + parser.add_argument( "-r", "--revision", dest="changeset_revision", required=True, help="Repository owner." ) + parser.add_argument( "--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section." ) + parser.add_argument( "--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created." ) + parser.add_argument( "--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]") + parser.add_argument( "--tool-deps", dest="install_tool_dependencies", action="store_true", default=False, help="Install tool dependencies. [False]" ) + options = parser.parse_args() + main( options )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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