Merge pull request #183 from ENCODE-DCC/dev

v2.2.2
ENCODE-DCC · Jul 25, 2022 · 2ff0999 · 2ff0999
2 parents 149142b + 4c23edf
commit 2ff0999
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Showing 4 changed files with 15 additions and 4 deletions.
diff --git a/caper/__init__.py b/caper/__init__.py
@@ -2,4 +2,4 @@
 from .caper_runner import CaperRunner
 
 __all__ = ['CaperClient', 'CaperClientSubmit', 'CaperRunner']
-__version__ = '2.2.1'
+__version__ = '2.2.2'
diff --git a/caper/caper_backend_conf.py b/caper/caper_backend_conf.py
@@ -255,6 +255,7 @@ def __init__(
                 sge_pe=sge_pe,
                 sge_queue=sge_queue,
                 sge_extra_param=sge_extra_param,
+                sge_resource_param=sge_resource_param,
             ),
         )
 
@@ -267,6 +268,7 @@ def __init__(
                 local_hash_strat=local_hash_strat,
                 pbs_queue=pbs_queue,
                 pbs_extra_param=pbs_extra_param,
+                pbs_resource_param=pbs_resource_param,
             ),
         )
 
@@ -279,6 +281,7 @@ def __init__(
                 local_hash_strat=local_hash_strat,
                 lsf_queue=lsf_queue,
                 lsf_extra_param=lsf_extra_param,
+                lsf_resource_param=lsf_resource_param,
             ),
         )
 

diff --git a/caper/cromwell.py b/caper/cromwell.py
@@ -37,9 +37,9 @@ class Cromwell:
     """Wraps Cromwell/Womtool.
     """
 
-    DEFAULT_CROMWELL = 'https://github.com/broadinstitute/cromwell/releases/download/65/cromwell-65.jar'
+    DEFAULT_CROMWELL = 'https://github.com/broadinstitute/cromwell/releases/download/82/cromwell-82.jar'
     DEFAULT_WOMTOOL = (
-        'https://github.com/broadinstitute/cromwell/releases/download/65/womtool-65.jar'
+        'https://github.com/broadinstitute/cromwell/releases/download/82/womtool-82.jar'
     )
     DEFAULT_CROMWELL_INSTALL_DIR = '~/.caper/cromwell_jar'
     DEFAULT_WOMTOOL_INSTALL_DIR = '~/.caper/womtool_jar'

diff --git a/caper/cromwell_backend.py b/caper/cromwell_backend.py
@@ -292,7 +292,12 @@ def default_runtime_attributes(self):
 
 
 class CromwellBackendGcp(CromwellBackendBase):
-    TEMPLATE = {'google': {'application-name': 'cromwell'}}
+    TEMPLATE = {
+        'google': {
+            'application-name': 'cromwell'
+        },
+        'engine': {'filesystems': {FILESYSTEM_GCS: {'auth': 'default'}}},
+    }
     TEMPLATE_BACKEND = {
         'config': {
             'default-runtime-attributes': {},
@@ -378,12 +383,14 @@ def __init__(
             with open(gcp_service_account_key_json) as fp:
                 key_json = json.loads(fp.read())
             genomics['compute-service-account'] = key_json['client_email']
+            self['engine']['filesystems'][FILESYSTEM_GCS]['auth'] = 'service-account'
         else:
             genomics['auth'] = 'application-default'
             filesystems[FILESYSTEM_GCS]['auth'] = 'application-default'
             self['google']['auths'] = [
                 {'name': 'application-default', 'scheme': 'application_default'}
             ]
+            self['engine']['filesystems'][FILESYSTEM_GCS]['auth'] = 'application-default'
 
         if use_google_cloud_life_sciences:
             self.backend['actor-factory'] = CromwellBackendGcp.ACTOR_FACTORY_V2BETA
@@ -396,6 +403,7 @@ def __init__(
                 self.default_runtime_attributes['zones'] = ' '.join(gcp_zones)
 
         config['project'] = gcp_prj
+        self['engine']['filesystems'][FILESYSTEM_GCS]['project'] = gcp_prj
 
         if not gcp_out_dir.startswith('gs://'):
             raise ValueError(