Mercurial > repos > bcclaywell > argo_navis

comparison venv/lib/python2.7/site-packages/planemo/galaxy_serve.py @ 0:d67268158946 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:d67268158946
1 import contextlib
2 import os
3
4 from planemo import galaxy_config
5 from planemo import galaxy_run
6 from planemo import io
7
8
9 def serve(ctx, paths, **kwds):
10 # TODO: Preceate a user.
11 # TODO: Setup an admin user.
12 # TODO: Pass through more parameters.
13 # TODO: Populate test-data directory as FTP directory.
14 daemon = kwds.get("daemon", False)
15 if daemon:
16 kwds["no_cleanup"] = True
17
18 with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
19 # TODO: Allow running dockerized Galaxy here instead.
20 run_script = os.path.join(config.galaxy_root, "run.sh")
21 if daemon:
22 run_script += " --daemon --wait"
23 config.env["GALAXY_RUN_ALL"] = "1"
24 else:
25 run_script += " --server-name '%s' --reload" % config.server_name
26 server_ini = os.path.join(config.config_directory, "galaxy.ini")
27 config.env["GALAXY_CONFIG_FILE"] = server_ini
28 cmds = [
29 run_script,
30 ]
31 cmd = "; ".join(cmds)
32 action = "Starting galaxy"
33 galaxy_run.run_galaxy_command(
34 ctx,
35 cmd,
36 config.env,
37 action,
38 )
39 return config
40
41
42 @contextlib.contextmanager
43 def shed_serve(ctx, install_args_list, **kwds):
44 config = serve(ctx, [], daemon=True, **kwds)
45 install_deps = not kwds.get("skip_dependencies", False)
46 try:
47 io.info("Installing repositories - this may take some time...")
48 for install_args in install_args_list:
49 install_args["install_tool_dependencies"] = install_deps
50 install_args["install_repository_dependencies"] = True
51 install_args["new_tool_panel_section_label"] = "Shed Installs"
52 config.install_repo(
53 **install_args
54 )
55 config.wait_for_all_installed()
56 yield config
57 finally:
58 config.kill()
59 if not kwds.get("no_cleanup", False):
60 config.cleanup()