Merge pull request #9170 from mvdbeek/try_sourcing_activate_d_scripts

[20.01] source /usr/local/etc/conda/activate.d/*.sh files

lib/galaxy/jobs/command_factory.py

@@ -85,7 +85,7 @@ def build_command(
             external_command_shell = container.shell
         else:
             external_command_shell = shell
-        externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params)
+        externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params, container=container)
         if container and modify_command_for_container:
             # Stop now and build command before handling metadata and copying
             # working directory files back. These should always happen outside
@@ -129,7 +129,7 @@ def build_command(
     return commands_builder.build()
 
 
-def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh"):
+def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh", container=None):
     local_container_script = join(job_wrapper.working_directory, script_name)
     tool_commands = commands_builder.build()
     config = job_wrapper.app.config
@@ -144,11 +144,15 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
     set_e = ""
     if job_wrapper.strict_shell:
         set_e = "set -e\n"
-    script_contents = u"#!%s\n%s%s%s" % (
+    source_command = ""
+    if container:
+        source_command = container.source_environment
+    script_contents = u"#!%s\n%s%s%s%s" % (
         shell,
         integrity_injection,
         set_e,
-        tool_commands
+        source_command,
+        tool_commands,
     )
     write_script(local_container_script, script_contents, config)
     commands = "%s %s" % (shell, local_container_script)

lib/galaxy/tool_util/deps/container_classes.py

@@ -56,6 +56,20 @@ if not found:
     subprocess.check_call(cmd, shell=True)
 EOF
 '''
+SOURCE_CONDA_ACTIVATE = """
+# Check if container was created by installing conda packages,
+# and if so, source scripts to populate environment variables
+# that would be set by activating the conda environment.
+if [ -d /usr/local/etc/conda/activate.d ]; then
+  export CONDA_PREFIX=/usr/local
+  for f in /usr/local/etc/conda/activate.d/*.sh; do
+    case "$f" in
+      "/usr/local/etc/conda/activate.d/activate-"*) :;;
+      *) . "$f" ;;
+    esac;
+  done
+fi
+"""
 
 
 @six.add_metaclass(ABCMeta)
@@ -83,6 +97,12 @@ class Container(object):
     def shell(self):
         return DEFAULT_CONTAINER_SHELL if not self.container_description else self.container_description.shell
 
+    @property
+    def source_environment(self):
+        if self.container_description and not self.container_description.explicit:
+            return SOURCE_CONDA_ACTIVATE
+        return ""
+
     @abstractmethod
     def containerize_command(self, command):
         """

lib/galaxy/tool_util/deps/container_resolvers/explicit.py

@@ -24,6 +24,7 @@ class ExplicitContainerResolver(ContainerResolver):
         """
         for container_description in tool_info.container_descriptions:
             if self._container_type_enabled(container_description, enabled_container_types):
+                container_description.explicit = True
                 return container_description
 
         return None

lib/galaxy/tool_util/deps/requirements.py

@@ -170,6 +170,7 @@ class ContainerDescription(object):
         self.type = type
         self.resolve_dependencies = resolve_dependencies
         self.shell = shell
+        self.explicit = False
 
     def to_dict(self, *args, **kwds):
         return dict(