Overhaul Conda support for recent Galaxy improvements.

Always set a condarc file up when using planemo - this is needed to fix channel handling for galaxy-lib update which sets up a $HOME for every conda command. Also update the list of default channels.

Author: jmchilton

planemo/commands/cmd_conda_env.py

@@ -43,7 +43,7 @@ def cli(ctx, path, **kwds):
         % which bowtie2
         TODO_PLACE_PATH_HERE
     """
-    conda_context = build_conda_context(use_planemo_shell_exec=False, **kwds)
+    conda_context = build_conda_context(ctx, use_planemo_shell_exec=False, **kwds)
     conda_targets = collect_conda_targets(
         path, conda_context=conda_context
     )

planemo/commands/cmd_conda_init.py

@@ -21,5 +21,5 @@ def cli(ctx, **kwds):
     license a 3-clause BSD 3 license. Please review full license at
     http://docs.continuum.io/anaconda/eula.
     """
-    conda_context = build_conda_context(**kwds)
+    conda_context = build_conda_context(ctx, **kwds)
     return conda_util.install_conda(conda_context=conda_context)

planemo/commands/cmd_conda_install.py

@@ -15,7 +15,7 @@
 @command_function
 def cli(ctx, path, **kwds):
     """Install conda packages for tool requirements."""
-    conda_context = build_conda_context(**kwds)
+    conda_context = build_conda_context(ctx, **kwds)
     return_codes = []
     for conda_target in collect_conda_targets(path):
         ctx.log("Install conda target %s" % conda_target)

planemo/conda.py

@@ -1,29 +1,37 @@
-""" Planemo specific utilities for dealing with conda, extending Galaxy's
-features with planemo specific idioms.
+"""Planemo specific utilities for dealing with conda.
+
+The extend Galaxy/galaxy-lib's features with planemo specific idioms.
 """
 from __future__ import absolute_import
 
+import os
+
 from galaxy.tools.deps import conda_util
 from galaxy.tools.deps.requirements import parse_requirements_from_xml
 from galaxy.tools.loader_directory import load_tool_elements_from_path
 
 from planemo.io import shell
 
 
-def build_conda_context(**kwds):
-    """ Build a Galaxy CondaContext tailored to planemo use
-    and common command-line arguments.
+def build_conda_context(ctx, **kwds):
+    """Build a galaxy-lib CondaContext tailored to planemo use.
+
+    Using planemo's common command-line/globa config options.
     """
+    condarc_override_default = os.path.join(ctx.workspace, "condarc")
     conda_prefix = kwds.get("conda_prefix", None)
     use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
     ensure_channels = kwds.get("conda_ensure_channels", "")
+    condarc_override = kwds.get("condarc", condarc_override_default)
     shell_exec = shell if use_planemo_shell else None
     return conda_util.CondaContext(conda_prefix=conda_prefix,
                                    ensure_channels=ensure_channels,
+                                   condarc_override=condarc_override,
                                    shell_exec=shell_exec)
 
 
 def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
+    """Load CondaTarget objects from supplied artifact sources."""
     conda_targets = []
     for (tool_path, tool_xml) in load_tool_elements_from_path(path):
         if found_tool_callback:

planemo/galaxy/config.py

@@ -180,7 +180,7 @@ def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
         def config_join(*args):
             return os.path.join(config_directory, *args)
 
-        _handle_dependency_resolution(config_directory, kwds)
+        _handle_dependency_resolution(ctx, config_directory, kwds)
         _handle_job_metrics(config_directory, kwds)
 
         shed_tool_conf = "config/shed_tool_conf.xml"
@@ -289,7 +289,7 @@ def config_join(*args):
             galaxy_root = config_join("galaxy-dev")
 
         server_name = "planemo%d" % random.randint(0, 100000)
-        _handle_dependency_resolution(config_directory, kwds)
+        _handle_dependency_resolution(ctx, config_directory, kwds)
         _handle_job_config_file(config_directory, server_name, kwds)
         _handle_job_metrics(config_directory, kwds)
         file_path = kwds.get("file_path") or config_join("files")
@@ -1118,7 +1118,7 @@ def _handle_job_config_file(config_directory, server_name, kwds):
     kwds["job_config_file"] = job_config_file
 
 
-def _handle_dependency_resolution(config_directory, kwds):
+def _handle_dependency_resolution(ctx, config_directory, kwds):
     resolutions_strategies = [
         "brew_dependency_resolution",
         "dependency_resolvers_config_file",
@@ -1149,16 +1149,19 @@ def _handle_dependency_resolution(config_directory, kwds):
     def add_attribute(key, value):
         attributes.append('%s="%s"' % (key, value))
 
+    conda_prefix_specified = False
     for key, default_value in iteritems(dependency_attribute_kwds):
         value = kwds.get(key, default_value)
         if value != default_value:
+            conda_prefix_specified = value == "conda_prefix"
             # Strip leading prefix (conda_) off attributes
             attribute_key = "_".join(key.split("_")[1:])
             add_attribute(attribute_key, value)
 
-    if not [attribute for attribute in attributes if "prefix" in attribute]:
-        conda_context = build_conda_context(**kwds)
+    conda_context = build_conda_context(ctx, **kwds)
+    if not conda_prefix_specified:
         add_attribute("prefix", conda_context.conda_prefix)
+    add_attribute("condarc_override", conda_context.condarc_override)
 
     attribute_str = " ".join(attributes)
 
@@ -1173,6 +1176,11 @@ def add_attribute(key, value):
                 'attributes': attribute_str
             })
             open(resolvers_conf, "w").write(conf_contents)
+            ctx.vlog(
+                "Writing dependency_resolvers_config_file to path %s with contents [%s]",
+                resolvers_conf,
+                conf_contents,
+            )
             kwds["dependency_resolvers_config_file"] = resolvers_conf
 
 

planemo/options.py

@@ -432,7 +432,7 @@ def conda_ensure_channels_option():
         use_global_config=True,
         help=("Ensure conda is configured with specified comma separated "
               "list of channels."),
-        default="r,bioconda"
+        default="r,bioconda,iuc",
     )