--- a/env/lib/python3.7/site-packages/planemo/galaxy/run.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-"""Utilities for calling Galaxy scripts."""
-import os
-import string
-
-from galaxy.tool_util.deps.commands import shell
-from six.moves import shlex_quote
-
-from planemo.io import info, shell_join
-from planemo.virtualenv import (
-    create_command,
-    DEFAULT_PYTHON_VERSION,
-)
-
-
-# Activate galaxy's virtualenv if present (needed for tests say but not for
-# server because run.sh does this).
-ACTIVATE_COMMAND = 'if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi'
-CREATE_COMMAND_TEMPLATE = string.Template(
-    'if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then $create_virtualenv; fi',
-)
-PRINT_VENV_COMMAND = shell_join(
-    r'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
-    ('if [ -e "$GALAXY_VIRTUAL_ENV" ]; '
-     'then echo "Virtual environment directory exists."; '
-     'else echo "Virtual environment directory does not exist."; fi'),
-)
-
-
-CACHED_VIRTUAL_ENV_COMMAND = ("if [ -d .venv ] || [ -f dist-eggs.ini ]; "
-                              "then GALAXY_VIRTUAL_ENV=.venv; "
-                              "else GALAXY_VIRTUAL_ENV=%s; fi")
-UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
-
-
-def setup_venv(ctx, kwds):
-    if kwds.get("skip_venv", False):
-        return ""
-
-    create_template_params = {
-        'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV", kwds.get('galaxy_python_version'))
-    }
-    return shell_join(
-        locate_galaxy_virtualenv(ctx, kwds),
-        PRINT_VENV_COMMAND if ctx.verbose else None,
-        CREATE_COMMAND_TEMPLATE.safe_substitute(create_template_params),
-        PRINT_VENV_COMMAND if ctx.verbose else None,
-        ACTIVATE_COMMAND,
-    )
-
-
-def locate_galaxy_virtualenv(ctx, kwds):
-    if os.environ.get("GALAXY_VIRTUAL_ENV"):
-        venv_command = ""
-    elif not kwds.get("no_cache_galaxy", False):
-        workspace = ctx.workspace
-        galaxy_branch = kwds.get("galaxy_branch") or "master"
-        shared_venv_path = os.path.join(workspace, "gx_venv")
-        galaxy_python_version = kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION
-        if galaxy_python_version != DEFAULT_PYTHON_VERSION:
-            shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_python_version)
-        if galaxy_branch != "master":
-            shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_branch)
-        venv_command = CACHED_VIRTUAL_ENV_COMMAND % shlex_quote(shared_venv_path)
-    else:
-        venv_command = UNCACHED_VIRTUAL_ENV_COMMAND
-    return shell_join(
-        venv_command,
-        "export GALAXY_VIRTUAL_ENV",
-    )
-
-
-def shell_if_wheels(command):
-    """ Take a shell command and convert it to shell command that runs
-    only if Galaxy is new enough to use wheels.
-    """
-    return "$(grep -q 'skip-venv' run_tests.sh) && %s" % command
-
-
-def setup_common_startup_args():
-    return _set_variable_if_wheels(
-        "COMMON_STARTUP_ARGS", "--dev-wheels"
-    )
-
-
-def _set_variable_if_wheels(var, if_wheels_val, else_val=""):
-    var_command = '${var}=${else_val}; '
-    var_command += shell_if_wheels(
-        '${var}="${if_wheels_val}"; '
-    )
-    var_command += "export ${var}"
-    var_command += '; echo "Set ${var} to ${${var}}"'
-    return string.Template(var_command).safe_substitute(
-        var=var,
-        if_wheels_val=if_wheels_val,
-        else_val=else_val,
-    )
-
-
-def run_galaxy_command(ctx, command, env, action):
-    """Run Galaxy command with informative verbose logging."""
-    message = "%s with command [%s]" % (action, command)
-    info(message)
-    ctx.vlog("With environment variables:")
-    ctx.vlog("============================")
-    for key, value in env.items():
-        ctx.vlog('%s="%s"' % (key, value))
-    ctx.vlog("============================")
-    exit_code = shell(command, env=env)
-    ctx.vlog("run command exited with return code %s" % exit_code)
-    return exit_code
-
-
-__all__ = (
-    "setup_venv",
-    "run_galaxy_command",
-    "setup_common_startup_args",
-)