Allow ``conda_install`` to work with packages as well as just tools.

galaxyproject · Feb 16, 2017 · 8faf661f70204ddd48945d583bcd95613a58ed0b · 8faf661
1 parent 9c790d0
commit 8faf661f70204ddd48945d583bcd95613a58ed0b
Unified Split

Showing with 53 additions and 3 deletions.

+3 −2 planemo/commands/cmd_conda_install.py

+24 −1 planemo/conda.py

+26 −0 planemo/options.py
diff --git a/planemo/commands/cmd_conda_install.py b/planemo/commands/cmd_conda_install.py
@@ -10,8 +10,9 @@
 @click.command('conda_install')
-  
-@options.optional_tools_arg(multiple=True)
+  
+@options.optional_tools_or_packages_arg(multiple=True)
 @options.conda_target_options()
+  
+@options.conda_global_option()
 @options.conda_auto_init_option()
 @command_function
 def cli(ctx, paths, **kwds):
@@ -21,7 +22,7 @@ def cli(ctx, paths, **kwds):
    for conda_target in collect_conda_targets(ctx, paths):
        ctx.log("Install conda target %s" % conda_target)
        return_code = conda_util.install_conda_target(
-  
-            conda_target, conda_context=conda_context
+  
+            conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False)
        )
        return_codes.append(return_code)
    return coalesce_return_codes(return_codes, assert_at_least_one=True)
diff --git a/planemo/conda.py b/planemo/conda.py
@@ -60,14 +60,37 @@ def collect_conda_targets(ctx, paths, found_tool_callback=None, conda_context=No
    appear once in the output.
    """
    conda_targets = set([])
-  
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths):
+  
+    real_paths = []
+  
+    for path in paths:
+  
+        if not os.path.exists(path):
+  
+            targets = target_str_to_targets(path)
+  
+            [conda_targets.add(_) for _ in targets]
+  
+        else:
+  
+            real_paths.append(path)
+  
+
+  
+    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, real_paths):
        if found_tool_callback:
            found_tool_callback(tool_path)
        for target in tool_source_conda_targets(tool_source):
            conda_targets.add(target)
    return conda_targets
+  
+# Copied and modified from mulled stuff - need to syncronize these concepts.
+  
+def target_str_to_targets(targets_raw):
+  
+    def parse_target(target_str):
+  
+        if "=" in target_str:
+  
+            package_name, version = target_str.split("=", 1)
+  
+        else:
+  
+            package_name = target_str
+  
+            version = None
+  
+        target = conda_util.CondaTarget(package_name, version)
+  
+        return target
+  
+
+  
+    targets = [parse_target(_) for _ in targets_raw.split(",")]
+  
+    return targets
+  
+
+  
+
 def collect_conda_target_lists(ctx, paths, found_tool_callback=None):
    """Load CondaTarget lists from supplied artifact sources.

diff --git a/planemo/options.py b/planemo/options.py
@@ -481,6 +481,18 @@ def conda_auto_init_option():
    )
+  
+def conda_global_option():
+  
+    return planemo_option(
+  
+        "--global",
+  
+        is_flag=True,
+  
+        default=False,
+  
+        help=("Install Conda dependencies globally instead of in requirement specific "
+  
+              "environments packaged for tools. If the Conda bin directory is on your "
+  
+              "PATH, tools may still use binaries but this is more designed for "
+  
+              "interactive testing and debugging.")
+  
+    )
+  
+
+  
+
 def required_tool_arg():
    """ Decorate click method as requiring the path to a single tool.
    """
@@ -514,6 +526,20 @@ def _optional_tools_default(ctx, param, value):
        return value
+  
+def optional_tools_or_packages_arg(multiple=False):
+  
+    """ Decorate click method as optionally taking in the path to a tool
+  
+    or directory of tools or a Conda package. If no such argument is given
+  
+    the current working directory will be treated as a directory of tools.
+  
+    """
+  
+    name = "paths" if multiple else "path"
+  
+    nargs = -1 if multiple else 1
+  
+    return click.argument(
+  
+        name,
+  
+        metavar="TARGET",
+  
+        nargs=nargs,
+  
+    )
+  
+
+  
+
 def optional_tools_arg(multiple=False):
    """ Decorate click method as optionally taking in the path to a tool
    or directory of tools. If no such argument is given the current working