v2.0.0

.circleci/config.yml

@@ -19,10 +19,10 @@ update_apt: &update_apt
     sudo apt-get update
 
 
-install_python3: &install_python3_java
-  name: Install python3, pip3, java
+install_python3: &install_python3
+  name: Install python3, pip3
   command: |
-    sudo apt-get install software-properties-common git wget curl default-jre -y
+    sudo apt-get install software-properties-common git wget curl -y
     sudo add-apt-repository ppa:deadsnakes/ppa -y
     sudo apt-get update && sudo apt-get install python3.6 -y
     sudo wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py
@@ -61,17 +61,26 @@ install_aws_lib: &install_aws_lib
     sudo pip3 install boto3 awscli
 
 
+install_java: &install_java
+  name: Install openjdk-11
+  command: |
+    sudo add-apt-repository ppa:openjdk-r/ppa -y
+    sudo apt-get update && sudo apt-get install openjdk-11-jdk -y
+    # automatically set 11 as default java
+    sudo update-java-alternatives -a
+
 jobs:
   pytest:
     <<: *machine_defaults
     steps:
       - checkout
       - run: *update_apt
-      - run: *install_python3_java
+      - run: *install_python3
       - run: *install_singularity
       - run: *install_py3_packages
       - run: *install_gcs_lib
       - run: *install_aws_lib
+      - run: *install_java
       - run:
           no_output_timeout: 60m
           command: |

caper/__init__.py

@@ -2,4 +2,4 @@
 from .caper_runner import CaperRunner
 
 __all__ = ['CaperClient', 'CaperClientSubmit', 'CaperRunner']
-__version__ = '1.6.3'
+__version__ = '2.0.0'

caper/caper_args.py

@@ -14,17 +14,17 @@
     LOCAL_HASH_STRAT_FILE,
     LOCAL_HASH_STRAT_PATH,
     LOCAL_HASH_STRAT_PATH_MTIME,
-    CromwellBackendAWS,
+    CromwellBackendAws,
     CromwellBackendBase,
     CromwellBackendCommon,
     CromwellBackendDatabase,
-    CromwellBackendGCP,
+    CromwellBackendGcp,
     CromwellBackendLocal,
+    CromwellBackendSlurm,
 )
 from .cromwell_rest_api import CromwellRestAPI
 from .resource_analysis import ResourceAnalysis
 from .server_heartbeat import ServerHeartbeat
-from .singularity import Singularity
 
 DEFAULT_CAPER_CONF = '~/.caper/default.conf'
 DEFAULT_LIST_FORMAT = 'id,status,name,str_label,user,parent,submission'
@@ -115,7 +115,7 @@ def get_parser_and_defaults(conf_file=None):
         'localized input JSON files due to deepcopying (recursive localization). '
         'Cromwell\'s MySQL/PostgreSQL DB password can be exposed on backend.conf '
         'on this directory. Therefore, DO NOT USE /tmp HERE. This directory is '
-        'also used for storing cached files for local/slurm/sge/pbs backends.',
+        'also used for storing cached files for local/slurm/sge/pbs/lsf backends.',
     )
     group_loc.add_argument(
         '--gcp-loc-dir',
@@ -278,7 +278,7 @@ def get_parser_and_defaults(conf_file=None):
         'does not allow hard-linking. e.g. beeGFS. '
         'This flag does not work with backends based on a Docker container. '
         'i.e. gcp and aws. Also, '
-        'it does not work with local backends (local/slurm/sge/pbs) '
+        'it does not work with local backends (local/slurm/sge/pbs/lsf) '
         'with --. However, it works fine with --singularity.',
     )
     group_cromwell.add_argument(
@@ -290,7 +290,7 @@ def get_parser_and_defaults(conf_file=None):
             LOCAL_HASH_STRAT_PATH_MTIME,
         ],
         help='File hashing strategy for call caching. '
-        'For local backends (local/slurm/sge/pbs) only. '
+        'For local backends (local/slurm/sge/pbs/lsf) only. '
         'file: use md5sum hash (slow), path: use path only, '
         'path+modtime (default): use path + mtime.',
     )
@@ -305,6 +305,14 @@ def get_parser_and_defaults(conf_file=None):
         'For gcp, define --gcp-out-dir. '
         'For aws, define --aws-out-dir.',
     )
+    group_local.add_argument(
+        '--slurm-resource-param',
+        help='SLURM resource parameters to be passed to sbatch. '
+        'You can customize this to fit your cluster\'s configuration. '
+        'You can use WDL syntax in ${} notation with Cromwell\'s built-in resource '
+        'variables. See documentation for details. ',
+        default=CromwellBackendSlurm.DEFAULT_SLURM_RESOURCE_PARAM,
+    )
 
     group_gc_all = parent_backend.add_argument_group(
         title='GCP backend arguments for server/runner/client'
@@ -325,7 +333,7 @@ def get_parser_and_defaults(conf_file=None):
     )
     group_gc.add_argument(
         '--gcp-region',
-        default=CromwellBackendGCP.DEFAULT_REGION,
+        default=CromwellBackendGcp.DEFAULT_REGION,
         help='GCP region for Google Cloud Life Sciences API. '
         'This is used only when --use-google-cloud-life-sciences is defined.',
     )
@@ -338,7 +346,7 @@ def get_parser_and_defaults(conf_file=None):
     )
     group_gc.add_argument(
         '--gcp-call-caching-dup-strat',
-        default=CromwellBackendGCP.DEFAULT_CALL_CACHING_DUP_STRAT,
+        default=CromwellBackendGcp.DEFAULT_CALL_CACHING_DUP_STRAT,
         choices=[CALL_CACHING_DUP_STRAT_REFERENCE, CALL_CACHING_DUP_STRAT_COPY],
         help='Duplication strategy for call-cached outputs for GCP backend: '
         'copy: make a copy, reference: refer to old output in metadata.json.',
@@ -360,7 +368,7 @@ def get_parser_and_defaults(conf_file=None):
     )
     group_aws.add_argument(
         '--aws-call-caching-dup-strat',
-        default=CromwellBackendAWS.DEFAULT_CALL_CACHING_DUP_STRAT,
+        default=CromwellBackendAws.DEFAULT_CALL_CACHING_DUP_STRAT,
         choices=[CALL_CACHING_DUP_STRAT_REFERENCE, CALL_CACHING_DUP_STRAT_COPY],
         help='Duplication strategy for call-cached outputs for AWS backend: '
         'copy: make a copy, reference: refer to old output in metadata.json.',
@@ -397,14 +405,6 @@ def get_parser_and_defaults(conf_file=None):
         action='store_true',
         help='Put a hold on a workflow when submitted to a Cromwell server.',
     )
-    parent_submit.add_argument(
-        '--singularity-cachedir',
-        default=Singularity.DEFAULT_SINGULARITY_CACHEDIR,
-        help='Singularity cache directory. Equivalent to exporting an '
-        'environment variable SINGULARITY_CACHEDIR. '
-        'Define it to prevent repeatedly building a singularity image '
-        'for every pipeline task',
-    )
     parent_submit.add_argument(
         '--use-gsutil-for-s3',
         action='store_true',
@@ -477,7 +477,7 @@ def get_parser_and_defaults(conf_file=None):
         description='Cloud-based backends (gc and aws) will only use Docker '
         'so that "--docker URI_FOR_DOCKER_IMG" must be specified '
         'in the command line argument or as a comment "#CAPER '
-        'docker URI_FOR_DOCKER_IMG" or value for "workflow.meta.caper_docker"'
+        'docker URI_FOR_DOCKER_IMG" or value for "workflow.meta.default_docker"'
         'in a WDL file',
     )
     group_dep.add_argument(
@@ -486,9 +486,9 @@ def get_parser_and_defaults(conf_file=None):
         const='',
         default=None,
         help='URI for Docker image (e.g. ubuntu:latest). '
-        'This can also be used as a flag to use Docker image address '
+        'This can also be used as a flag to use Docker image URI '
         'defined in your WDL file as a comment ("#CAPER docker") or '
-        'as "workflow.meta.caper_docker" in WDL.',
+        'as "workflow.meta.default_docker" in WDL.',
     )
     group_dep_local = parent_submit.add_argument_group(
         title='dependency resolver for local backend',
@@ -505,21 +505,26 @@ def get_parser_and_defaults(conf_file=None):
         help='URI or path for Singularity image '
         '(e.g. ~/.singularity/ubuntu-latest.simg, '
         'docker://ubuntu:latest, shub://vsoch/hello-world). '
-        'This can also be used as a flag to use Docker image address '
+        'This can also be used as a flag to use Singularity image URI '
         'defined in your WDL file as a comment ("#CAPER singularity") or '
-        'as "workflow.meta.caper_singularity" in WDL.',
+        'as "workflow.meta.default_singularity" in WDL.',
     )
     group_dep_local.add_argument(
-        '--no-build-singularity',
-        action='store_true',
-        help='Do not build singularity image before running a workflow. ',
+        '--conda',
+        nargs='?',
+        const='',
+        default=None,
+        help='Default Conda environment\'s name. '
+        'If defined each task in WDL will be called with conda run -n ENV_NAME.'
+        'This can also be used as a flag to use Conda environment '
+        'defined in your WDL file under "workflow.meta.default_conda".',
     )
 
     group_slurm = parent_submit.add_argument_group('SLURM arguments')
     group_slurm.add_argument('--slurm-partition', help='SLURM partition')
     group_slurm.add_argument('--slurm-account', help='SLURM account')
     group_slurm.add_argument(
-        '--slurm-extra-param', help='SLURM extra parameters. Must be double-quoted'
+        '--slurm-extra-param', help='SLURM extra parameters to be passed to sbatch. '
     )
 
     group_sge = parent_submit.add_argument_group('SGE arguments')
@@ -537,6 +542,12 @@ def get_parser_and_defaults(conf_file=None):
         '--pbs-extra-param', help='PBS extra parameters. Must be double-quoted'
     )
 
+    group_lsf = parent_submit.add_argument_group('LSF arguments')
+    group_lsf.add_argument('--lsf-queue', help='LSF queue')
+    group_lsf.add_argument(
+        '--lsf-extra-param', help='LSF extra parameters. Must be double-quoted'
+    )
+
     # server
     parent_server = argparse.ArgumentParser(add_help=False)
     parent_server.add_argument(

caper/caper_backend_conf.py

@@ -8,15 +8,16 @@
     BACKEND_AWS,
     BACKEND_GCP,
     BACKEND_SGE,
-    CromwellBackendAWS,
+    CromwellBackendAws,
     CromwellBackendBase,
     CromwellBackendCommon,
     CromwellBackendDatabase,
-    CromwellBackendGCP,
+    CromwellBackendGcp,
     CromwellBackendLocal,
-    CromwellBackendPBS,
-    CromwellBackendSGE,
-    CromwellBackendSLURM,
+    CromwellBackendLsf,
+    CromwellBackendPbs,
+    CromwellBackendSge,
+    CromwellBackendSlurm,
 )
 from .dict_tool import merge_dict
 from .hocon_string import HOCONString
@@ -53,23 +54,29 @@ def __init__(
         file_db=None,
         gcp_prj=None,
         gcp_out_dir=None,
-        gcp_call_caching_dup_strat=CromwellBackendGCP.DEFAULT_CALL_CACHING_DUP_STRAT,
+        gcp_call_caching_dup_strat=CromwellBackendGcp.DEFAULT_CALL_CACHING_DUP_STRAT,
         gcp_service_account_key_json=None,
         use_google_cloud_life_sciences=False,
-        gcp_region=CromwellBackendGCP.DEFAULT_REGION,
+        gcp_region=CromwellBackendGcp.DEFAULT_REGION,
         aws_batch_arn=None,
         aws_region=None,
         aws_out_dir=None,
-        aws_call_caching_dup_strat=CromwellBackendAWS.DEFAULT_CALL_CACHING_DUP_STRAT,
+        aws_call_caching_dup_strat=CromwellBackendAws.DEFAULT_CALL_CACHING_DUP_STRAT,
         gcp_zones=None,
         slurm_partition=None,
         slurm_account=None,
         slurm_extra_param=None,
+        slurm_resource_param=CromwellBackendSlurm.DEFAULT_SLURM_RESOURCE_PARAM,
         sge_pe=None,
         sge_queue=None,
         sge_extra_param=None,
+        sge_resource_param=CromwellBackendSge.DEFAULT_SGE_RESOURCE_PARAM,
         pbs_queue=None,
         pbs_extra_param=None,
+        pbs_resource_param=CromwellBackendPbs.DEFAULT_PBS_RESOURCE_PARAM,
+        lsf_queue=None,
+        lsf_extra_param=None,
+        lsf_resource_param=CromwellBackendLsf.DEFAULT_LSF_RESOURCE_PARAM,
     ):
         """Initializes the backend conf's stanzas.
 
@@ -93,7 +100,7 @@ def __init__(
             max_concurrent_tasks:
                 Limit for concurrent number of tasks for each workflow.
             soft_glob_output:
-                Local backends only (Local, sge, pbs, slurm).
+                Local backends only (Local, sge, pbs, slurm, lsf).
                 Glob with ln -s instead of hard-linking (ln alone).
                 Useful for file-system like beeGFS, which does not allow hard-linking.
             local_hash_strat:
@@ -166,11 +173,21 @@ def __init__(
             slurm_partition:
             slurm_account:
             slurm_extra_param:
+            slurm_resource_param:
+                For slurm backend only.
+                Resource parameters to be passed to sbatch.
+                You can use WDL syntax and Cromwell's built-in variables in ${} notation.
+                e.g. cpu, time, memory_mb
             sge_pe:
             sge_queue:
             sge_extra_param:
+            sge_resource_param:
             pbs_queue:
             pbs_extra_param:
+            pbs_resource_param:
+            lsf_queue:
+            lsf_extra_param:
+            lsf_resource_param:
         """
         self._template = {}
 
@@ -216,20 +233,21 @@ def __init__(
 
         merge_dict(
             self._template,
-            CromwellBackendSLURM(
+            CromwellBackendSlurm(
                 local_out_dir=local_out_dir,
                 max_concurrent_tasks=max_concurrent_tasks,
                 soft_glob_output=soft_glob_output,
                 local_hash_strat=local_hash_strat,
                 slurm_partition=slurm_partition,
                 slurm_account=slurm_account,
                 slurm_extra_param=slurm_extra_param,
+                slurm_resource_param=slurm_resource_param,
             ),
         )
 
         merge_dict(
             self._template,
-            CromwellBackendSGE(
+            CromwellBackendSge(
                 local_out_dir=local_out_dir,
                 max_concurrent_tasks=max_concurrent_tasks,
                 soft_glob_output=soft_glob_output,
@@ -242,7 +260,7 @@ def __init__(
 
         merge_dict(
             self._template,
-            CromwellBackendPBS(
+            CromwellBackendPbs(
                 local_out_dir=local_out_dir,
                 max_concurrent_tasks=max_concurrent_tasks,
                 soft_glob_output=soft_glob_output,
@@ -252,6 +270,18 @@ def __init__(
             ),
         )
 
+        merge_dict(
+            self._template,
+            CromwellBackendLsf(
+                local_out_dir=local_out_dir,
+                max_concurrent_tasks=max_concurrent_tasks,
+                soft_glob_output=soft_glob_output,
+                local_hash_strat=local_hash_strat,
+                lsf_queue=lsf_queue,
+                lsf_extra_param=lsf_extra_param,
+            ),
+        )
+
         # cloud backends
         if gcp_prj and gcp_out_dir:
             if gcp_service_account_key_json:
@@ -267,7 +297,7 @@ def __init__(
 
             merge_dict(
                 self._template,
-                CromwellBackendGCP(
+                CromwellBackendGcp(
                     max_concurrent_tasks=max_concurrent_tasks,
                     gcp_prj=gcp_prj,
                     gcp_out_dir=gcp_out_dir,
@@ -282,7 +312,7 @@ def __init__(
         if aws_batch_arn and aws_region and aws_out_dir:
             merge_dict(
                 self._template,
-                CromwellBackendAWS(
+                CromwellBackendAws(
                     max_concurrent_tasks=max_concurrent_tasks,
                     aws_batch_arn=aws_batch_arn,
                     aws_region=aws_region,