1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/921ad3745ba3/ Changeset: 921ad3745ba3 User: greg Date: 2013-05-22 20:36:08 Summary: Delete the original copy of the install_repository_tools.py Galaxy API script since it has been renamed to install_tool_shed_repositories.py Affected #: 1 file

diff -r 2a630237801ffefdd63e47c5acdcc1abadba23ef -r 921ad3745ba304aed12b0d3425cf9c6f9b727f7c scripts/api/install_repository_tools.py --- a/scripts/api/install_repository_tools.py +++ /dev/null @@ -1,52 +0,0 @@ -#!/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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