Allow PLANEMO_CONDA_PREFIX to be set a default for --conda_prefix.

A few other options too that might be useful - along with a framework enhancement for options to make this easy and regular.

Author: jmchilton

planemo/config.py

@@ -72,6 +72,7 @@ def planemo_option(*args, **kwargs):
     """
     option_type = kwargs.get("type", None)
     use_global_config = kwargs.pop("use_global_config", False)
+    use_env_var = kwargs.pop("use_env_var", False)
 
     if "default" in kwargs:
         default = kwargs.pop("default")
@@ -93,7 +94,16 @@ def callback(ctx, param, value):
         kwargs["callback"] = callback
         kwargs["default"] = None
 
-    return click.option(*args, **kwargs)
+    if use_env_var:
+        name = None
+        for arg in args:
+            if arg.startswith("--"):
+                name = arg[len("--"):]
+        assert name
+        kwargs["envvar"] = "PLANEMO_%s" % name.upper()
+
+    option = click.option(*args, **kwargs)
+    return option
 
 
 def global_config_path(config_path=None):

planemo/options.py

@@ -49,6 +49,7 @@ def serve_engine_option():
         type=click.Choice(["galaxy", "docker_galaxy"]),
         default="galaxy",
         use_global_config=True,
+        use_env_var=True,
         help=("Select an engine to serve aritfacts such as tools "
               "and workflows. Defaults to a local Galaxy, but running Galaxy within "
               "a Docker container.")
@@ -102,6 +103,7 @@ def galaxy_email_option():
         type=str,
         default="planemo@galaxyproject.org",
         use_global_config=True,
+        use_env_var=True,
         help="E-mail address to use when launching single-user Galaxy server.",
     )
 
@@ -119,6 +121,7 @@ def galaxy_database_seed_option():
         "--galaxy_database_seed",
         default=None,
         use_global_config=True,
+        use_env_var=True,
         type=click.Path(exists=True, file_okay=True, resolve_path=True),
         help="Preseeded Galaxy sqlite database to target.",
     )
@@ -403,6 +406,7 @@ def conda_prefix_option():
     return planemo_option(
         "--conda_prefix",
         use_global_config=True,
+        use_env_var=True,
         type=click.Path(file_okay=False, dir_okay=True),
         help="Conda prefix to use for conda dependency commands."
     )
@@ -430,6 +434,7 @@ def conda_ensure_channels_option():
         "--conda_ensure_channels",
         type=str,
         use_global_config=True,
+        use_env_var=True,
         help=("Ensure conda is configured with specified comma separated "
               "list of channels."),
         default="r,bioconda,iuc",