diff --git a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
index a8e3bb3204f..3ccd7ab7db8 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
@@ -2,6 +2,7 @@
+ ucsc-fatotwobit
ucsc_tools
faToTwoBit '$input' '$output'
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 34a34b37f31..ba8ee6ce1a2 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1306,7 +1306,7 @@ class Tool( object, Dictifiable ):
visit_input_values( self.inputs, values, validate_inputs )
return messages
- def build_dependency_cache(self):
+ def build_dependency_cache(self, **kwds):
if isinstance(self.app.toolbox.dependency_manager, CachedDependencyManager):
self.app.toolbox.dependency_manager.build_cache(
requirements=self.requirements,
@@ -1314,7 +1314,8 @@ class Tool( object, Dictifiable ):
tool_dir=self.tool_dir,
job_directory=None,
metadata=False,
- tool_instance=self
+ tool_instance=self,
+ **kwds
)
def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py
index 4f0a6d2a7d4..640726f73d9 100644
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tools/deps/__init__.py
@@ -5,6 +5,7 @@ Dependency management for tools.
import json
import logging
import os.path
+import shutil
from collections import OrderedDict
@@ -175,6 +176,12 @@ class CachedDependencyManager(DependencyManager):
resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
cacheable_dependencies = [dep for req, dep in resolved_dependencies.items() if dep.cacheable]
hashed_requirements_dir = self.get_hashed_requirements_path(cacheable_dependencies)
+ if kwds.get('force_rebuild', False) and os.path.exists(hashed_requirements_dir):
+ try:
+ shutil.rmtree(hashed_requirements_dir)
+ except Exception:
+ log.warning("Could not delete cached requirements directory '%s'" % hashed_requirements_dir)
+ pass
[dep.build_cache(hashed_requirements_dir) for dep in cacheable_dependencies]
def dependency_shell_commands( self, requirements, **kwds ):
diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py
index 42ddc44f77d..47f1b090006 100644
--- a/lib/galaxy/tools/deps/conda_util.py
+++ b/lib/galaxy/tools/deps/conda_util.py
@@ -214,6 +214,17 @@ class CondaContext(installable.InstallableContext):
install_base_args.extend(args)
return self.exec_command("install", install_base_args)
+ def exec_clean(self, args=[]):
+ """
+ Clean up after conda installation.
+ """
+ clean_base_args = [
+ "--tarballs",
+ "-y"
+ ]
+ clean_base_args.extend(args)
+ return self.exec_command("clean", clean_base_args)
+
def export_list(self, name, path):
return self.exec_command("list", [
"--name", name,
@@ -488,6 +499,7 @@ def build_isolated_environment(
return (path or tempdir_name, exit_code)
finally:
+ conda_context.exec_clean()
shutil.rmtree(tempdir)
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index 5751212626e..a21a37ebd4a 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -98,6 +98,9 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
self.auto_install = auto_install
self.copy_dependencies = copy_dependencies
+ def clean(self, **kwds):
+ return self.conda_context.exec_clean()
+
def resolve(self, name, version, type, **kwds):
# Check for conda just not being there, this way we can enable
# conda by default and just do nothing in not configured.
diff --git a/lib/galaxy/tools/deps/views.py b/lib/galaxy/tools/deps/views.py
index be4be6458b3..8f23335d7df 100644
--- a/lib/galaxy/tools/deps/views.py
+++ b/lib/galaxy/tools/deps/views.py
@@ -127,3 +127,15 @@ class DependencyResolversView(object):
def get_requirements_status(self, requested_requirements, installed_tool_dependencies=None):
return [self.manager_dependency(installed_tool_dependencies=installed_tool_dependencies, **req) for req in requested_requirements]
+
+ def clean(self, index=None, **kwds):
+ if index:
+ resolver = self._dependency_resolver(index)
+ if not hasattr(resolver, "clean"):
+ raise NotImplemented()
+ else:
+ resolver.clean()
+ return "OK"
+ else:
+ [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, 'clean')]
+ return "OK"
diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
index f91c93ff5a5..ea5821dfea3 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
@@ -162,3 +162,22 @@ class ToolDependenciesAPIController( BaseAPIController ):
the corresponding resolver (keyed on 'index').
"""
return self._view.manager_requirements()
+
+ @expose_api
+ @require_admin
+ def clean(self, trans, id=None, **kwds):
+ """
+ POST /api/dependencies_resolver/{index}/clean
+
+ Cleans up intermediate files created by resolvers during the dependency
+ installation.
+
+ :type index: int
+ :param index: index of the dependency resolver
+
+ :rtype: dict
+ :returns: a dictified description of the requirement that could
+ be resolved (keyed on 'requirement') and the index of
+ the corresponding resolver (keyed on 'index').
+ """
+ return self._view.clean(id, **kwds)
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 8dc7372738c..b76dd9a3f40 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -129,6 +129,40 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
tool = self._get_tool(id)
return tool.tool_requirements_status
+ @expose_api
+ @web.require_admin
+ def install_dependencies(self, trans, id, **kwds):
+ """
+ POST /api/tools/{tool_id}/install_dependencies
+ Attempts to install requirements via the dependency resolver
+
+ parameters:
+ build_dependency_cache: If true, attempts to cache dependencies for this tool
+ force_rebuild: If true and chache dir exists, attempts to delete cache dir
+ """
+ tool = self._get_tool(id)
+ [tool._view.install_dependency(id=None, **req.to_dict()) for req in tool.requirements]
+ if kwds.get('build_dependency_cache'):
+ tool.build_dependency_cache(**kwds)
+ # TODO: rework resolver install system to log and report what has been done.
+ # _view.install_dependency should return a dict with stdout, stderr and success status
+ return tool.tool_requirements_status
+
+ @expose_api
+ @web.require_admin
+ def build_dependency_cache(self, trans, id, **kwds):
+ """
+ POST /api/tools/{tool_id}/build_dependency_cache
+ Attempts to cache installed dependencies.
+
+ parameters:
+ force_rebuild: If true and chache dir exists, attempts to delete cache dir
+ """
+ tool = self._get_tool(id)
+ tool.build_dependency_cache(**kwds)
+ # TODO: Should also have a more meaningful return.
+ return tool.tool_requirements_status
+
@expose_api
@web.require_admin
def diagnostics( self, trans, id, **kwd ):
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 53d0c948383..8bee0a15ddb 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -262,12 +262,16 @@ def populate_api_routes( webapp, app ):
webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}/download', action='download', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}/requirements', action='requirements', controller="tools")
+ webapp.mapper.connect( '/api/tools/{id:.+?}/install_dependencies', action='install_dependencies', controller="tools", conditions=dict( method=[ "POST" ] ))
+ webapp.mapper.connect( '/api/tools/{id:.+?}/build_dependency_cache', action='build_dependency_cache', controller="tools", conditions=dict( method=[ "POST" ] ))
webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" )
webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' )
+ webapp.mapper.connect( '/api/dependency_resolvers/clean', action="clean", controller="tool_dependencies", conditions=dict( method=[ "POST" ]) )
webapp.mapper.connect( '/api/dependency_resolvers/dependency', action="manager_dependency", controller="tool_dependencies", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( '/api/dependency_resolvers/dependency', action="install_dependency", controller="tool_dependencies", conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( '/api/dependency_resolvers/requirements', action="manager_requirements", controller="tool_dependencies" )
+ webapp.mapper.connect( '/api/dependency_resolvers/{id}/clean', action="clean", controller="tool_dependencies", conditions=dict( method=[ "POST" ]) )
webapp.mapper.connect( '/api/dependency_resolvers/{id}/dependency', action="resolver_dependency", controller="tool_dependencies", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( '/api/dependency_resolvers/{id}/dependency', action="install_dependency", controller="tool_dependencies", conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( '/api/dependency_resolvers/{id}/requirements', action="resolver_requirements", controller="tool_dependencies" )
diff --git a/test/integration/test_resolvers.py b/test/integration/test_resolvers.py
index f1ee7d9b8eb..5b134ac54ee 100644
--- a/test/integration/test_resolvers.py
+++ b/test/integration/test_resolvers.py
@@ -17,6 +17,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase, A
@classmethod
def handle_galaxy_config_kwds(cls, config):
cls.conda_tmp_prefix = mkdtemp()
+ config["use_cached_dep_manager"] = True
config["conda_auto_init"] = True
config["conda_prefix"] = os.path.join(cls.conda_tmp_prefix, 'conda')
@@ -82,3 +83,22 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase, A
self._assert_status_code_is( create_response, 200 )
response = create_response.json()
assert response['dependency_type'] == 'conda' and not response['exact']
+
+ def test_conda_install_through_tools_api( self ):
+ tool_id = 'mulled_example_multi_1'
+ endpoint = "tools/%s/install_dependencies" % tool_id
+ data = {'id': tool_id}
+ create_response = self._post(endpoint, data=data, admin=True)
+ self._assert_status_code_is( create_response, 200 )
+ response = create_response.json()
+ assert any([True for d in response if d['dependency_type'] == 'conda'])
+ endpoint = "tools/%s/build_dependency_cache" % tool_id
+ create_response = self._post(endpoint, data=data, admin=True)
+ self._assert_status_code_is( create_response, 200 )
+
+ def test_conda_clean( self ):
+ endpoint = 'dependency_resolvers/clean'
+ create_response = self._post(endpoint, data={}, admin=True)
+ self._assert_status_code_is(create_response, 200)
+ response = create_response.json()
+ assert response == "OK"