diff --git a/planemo/galaxy_config.py b/planemo/galaxy_config.py index a93356dd7..05640cb54 100644 --- a/planemo/galaxy_config.py +++ b/planemo/galaxy_config.py @@ -136,8 +136,10 @@ def config_join(*args): config_directory = mkdtemp() try: latest_galaxy = False + install_env = {} if install_galaxy: - _install_galaxy(ctx, config_directory, kwds) + _build_eggs_cache(ctx, install_env, kwds) + _install_galaxy(ctx, config_directory, install_env, kwds) latest_galaxy = True galaxy_root = config_join("galaxy-dev") @@ -235,8 +237,7 @@ def config_join(*args): # retry_job_output_collection = 0 env = _build_env_for_galaxy(properties, template_args) - if install_galaxy: - _build_eggs_cache(ctx, env, kwds) + env.update(install_env) _build_test_env(properties, env) env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf @@ -534,25 +535,25 @@ def _shed_tool_conf(install_galaxy, config_directory): return os.path.join(config_dir, "shed_tool_conf.xml") -def _install_galaxy(ctx, config_directory, kwds): +def _install_galaxy(ctx, config_directory, env, kwds): if not kwds.get("no_cache_galaxy", False): - _install_galaxy_via_git(ctx, config_directory, kwds) + _install_galaxy_via_git(ctx, config_directory, env, kwds) else: - _install_galaxy_via_download(ctx, config_directory, kwds) + _install_galaxy_via_download(ctx, config_directory, env, kwds) -def _install_galaxy_via_download(ctx, config_directory, kwds): +def _install_galaxy_via_download(ctx, config_directory, env, kwds): branch = _galaxy_branch(kwds) tar_cmd = "tar -zxvf %s" % branch command = galaxy_run.DOWNLOAD_GALAXY + "; %s | tail" % tar_cmd - _install_with_command(ctx, config_directory, command, kwds) + _install_with_command(ctx, config_directory, command, env, kwds) -def _install_galaxy_via_git(ctx, config_directory, kwds): +def _install_galaxy_via_git(ctx, config_directory, env, kwds): gx_repo = _ensure_galaxy_repository_available(ctx, kwds) branch = _galaxy_branch(kwds) command = git.command_clone(ctx, gx_repo, "galaxy-dev", branch=branch) - _install_with_command(ctx, config_directory, command, kwds) + _install_with_command(ctx, config_directory, command, env, kwds) def _build_eggs_cache(ctx, env, kwds): @@ -587,7 +588,7 @@ def _galaxy_source(kwds): return source -def _install_with_command(ctx, config_directory, command, kwds): +def _install_with_command(ctx, config_directory, command, env, kwds): # TODO: --watchdog pip_installs = [] if kwds.get("cwl", False): @@ -606,7 +607,7 @@ def _install_with_command(ctx, config_directory, command, kwds): galaxy_run.setup_common_startup_args(), COMMAND_STARTUP_COMMAND, ) - shell(install_cmd) + shell(install_cmd, env=env) def _ensure_galaxy_repository_available(ctx, kwds):