From 6d0f50274df26defe4606c116e108a4f94d0e453 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 13 Jan 2016 17:27:23 +0000
Subject: [PATCH] Fix regression (egg caching broke against master/15.10).
Closes #396.
---
planemo/galaxy_config.py | 25 +++++++++++++------------
1 file changed, 13 insertions(+), 12 deletions(-)
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):