1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/31714646a7b4/ Changeset: 31714646a7b4 User: greg Date: 2013-05-24 21:14:08 Summary: Add some important documentation to some tool shed methods. Affected #: 2 files
diff -r 308719efff061598955f5b54fae2621c4f902ee9 -r 31714646a7b441f34a43748065278a1b08940c3c lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -798,12 +798,13 @@ label='Valid tools' ) containers_dict[ 'valid_tools' ] = valid_tools_root_folder # Tool test results container. - if tool_test_results: - # Only create and populate this folder if there are actual tool test results to display, since the - # display of the 'Test environment' folder by itself can be misleading. - if len( tool_test_results ) > 1: - folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) - containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder + if tool_test_results and len( tool_test_results ) > 1: + # Only create and populate this folder if there are actual tool test results to display, since the display of the 'Test environment' + # folder by itself can be misleading. We check for more than a single entry in the tool_test_results dictionary because it may have + # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", "installation_errors", "missing_test_components" + # "skipped_tests", "not_tested" or any other entry that may be added in the future. + folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) + containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. if metadata: if 'workflows' in metadata:
diff -r 308719efff061598955f5b54fae2621c4f902ee9 -r 31714646a7b441f34a43748065278a1b08940c3c lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -51,6 +51,70 @@ return output.return_code
def handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ): + """ + This method works with with a combination of three tool dependency definition tag sets, which are defined in the tool_dependencies.xml file in the + order discussed here. The example for this discussion is the tool_dependencies.xml file contained in the osra repository, which is available at: + + http://testtoolshed.g2.bx.psu.edu/view/bgruening/osra + + The first tag set defines a complex repository dependency like this. This tag set ensures that changeset revision XXX of the repository named + package_graphicsmagick_1_3 owned by YYY in the tool shed ZZZ has been previously installed. + + <tool_dependency> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" prior_installation_required="True" toolshed="ZZZ" /> + </package> + ... + + * By the way, there is an env.sh file associated with version 1.3.18 of the graphicsmagick package which looks something like this (we'll reference + this file later in this discussion. + ---- + GRAPHICSMAGICK_ROOT_DIR=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick; + export GRAPHICSMAGICK_ROOT_DIR + ---- + + The second tag set defines a specific package dependency that has been previously installed (guaranteed by the tag set discussed above) and compiled, + where the compiled dependency is needed by the tool dependency currently being installed (osra version 2.0.0 in this case) and complied in order for + it's installation and compilation to succeed. This tag set is contained within the <package name="osra" version="2.0.0"> tag set, which implies that + version 2.0.0 of the osra package requires version 1.3.18 of the graphicsmagick package in order to successfully compile. When this tag set is handled, + one of the effects is that the env.sh file associated with graphicsmagick version 1.3.18 is "sourced", which undoubtedly sets or alters certain environment + variables (e.g. PATH, PYTHONPATH, etc). + + <!-- populate the environment variables from the dependent repositories --> + <action type="set_environment_for_install"> + <repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" toolshed="ZZZ"> + <package name="graphicsmagick" version="1.3.18" /> + </repository> + </action> + + The third tag set enables discovery of the same required package dependency discussed above for correctly compiling the osra version 2.0.0 package, but + in this case the package can be discovered at tool execution time. Using the $ENV[] option as shown in this example, the value of the environment + variable named GRAPHICSMAGICK_ROOT_DIR (which was set in the environment using the second tag set described above) will be used to automatically alter + the env.sh file associated with the osra version 2.0.0 tool dependency when it is installed into Galaxy. * Refer to where we discussed the env.sh file + for version 1.3.18 of the graphicsmagick package above. + + <action type="set_environment"> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[$GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> + <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> + </action> + + The above tag will produce an env.sh file for version 2.0.0 of the osra package when it it installed into Galaxy that looks something like this. Notice + that the path to the gmagick binary is included here since it expands the defined $ENV[$GRAPHICSMAGICK_ROOT_DIR] value in the above tag set. + + ---- + LD_LIBRARY_PATH=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick/lib/:$LD_LIBRARY_PATH; + export LD_LIBRARY_PATH + LD_LIBRARY_PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/potrace/build/lib/:$LD_LIBRARY_PATH; + export LD_LIBRARY_PATH + PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/bin:$PATH; + export PATH + OSRA_DATA_FILES=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/share; + export OSRA_DATA_FILES + ---- + """ env_var_value = env_var_dict[ 'value' ] if '$ENV[' in env_var_value and ']' in env_var_value: # Pull out the name of the environment variable to populate. @@ -107,6 +171,8 @@ filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] if 'target_filename' in action_dict: + # Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this + # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. downloaded_filename = action_dict[ 'target_filename' ] else: downloaded_filename = os.path.split( url )[ -1 ] @@ -137,6 +203,8 @@ filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] if action_dict[ 'target_filename' ]: + # Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this + # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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