Merge pull request #130 from brinkmanlab/local-tools

Add tool_deps tool to allow triggering installation of local tool dep…

Author: mvdbeek

docs/commands.rst

@@ -10,5 +10,6 @@ Commands
    commands/run-data-managers
    commands/setup-data-libraries
    commands/shed-tools
+   commands/install-tool-deps
    commands/workflow-install
    commands/workflow-to-tools

docs/commands/install-tool-deps.rst

@@ -0,0 +1,12 @@
+Install-tool-deps
+=================
+
+.. automodule :: ephemeris.tool_deps
+
+Usage
+----------
+
+.. argparse::
+   :module: ephemeris.tool_deps
+   :func: _parser
+   :prog: install-tool-deps

src/ephemeris/install_tool_deps.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+'''Tool to install tool dependencies on a Galaxy instance.'''
+import argparse
+import os
+import xml.etree.ElementTree as ET
+
+import yaml
+from bioblend.galaxy.tools import ToolClient
+
+from ephemeris import get_galaxy_connection
+from ephemeris.common_parser import get_common_args
+
+
+def _parser():
+    parent = get_common_args()
+    parser = argparse.ArgumentParser(parents=[parent])
+    parser.add_argument("-t", "--tool", help='Path to a tool file, tool_conf file, or yaml file containing sequence of tool ids', nargs='*')
+    parser.add_argument("-i", "--id", help='Comma seperated list of tool ids', nargs='*')
+
+    return parser
+
+
+def main():
+    """
+    This script uses bioblend to trigger dependencies installations for the provided tools
+    """
+    args = _parser().parse_args()
+    gi = get_galaxy_connection(args)
+    tool_client = ToolClient(gi)
+
+    for tool_conf_path in args.tool:  # type: str
+        _, ext = os.path.splitext(tool_conf_path)
+        if (ext == '.xml'):
+            # install all
+            root = ET.ElementTree(file=tool_conf_path).getroot()
+            if root.tag == "toolbox":
+                # Install all from tool_conf
+                tool_path = root.get('tool_path', '')
+                tool_path.replace('${tool_conf_dir}', os.path.abspath(args.tool))
+                for tool in root.findall("tool[@file]"):
+                    tool_id = ET.ElementTree(file=tool.get('file')).getroot().get('id')
+                    if tool_id:
+                        tool_client.install_dependencies(tool_id)
+            elif root.tag == "tool" and root.get('id'):
+                # Install from single tool file
+                tool_client.install_dependencies(root.get('id'))
+        else:
+            for tool_id in yaml.safe_load(tool_conf_path):
+                # Install from yaml file
+                tool_client.install_dependencies(tool_id)
+
+    for tool_id in args.id:  # type: str
+        tool_client.install_dependencies(tool_id.strip())
+
+
+if __name__ == '__main__':
+    main()