Added support for udocker

MaBoSS/src/MaBoSS_BB/definitions.py

@@ -4,10 +4,19 @@
 
 # Do not change this line
 BB_SOURCE_PATH=os.path.dirname(os.path.abspath(__file__))
+CONTAINER_ENGINE = os.environ["CONTAINER_ENGINE"]
 
 # Update the following lines:
 #  - Assets folder within the Building Block
 ASSETS_PATH = os.path.join(BB_SOURCE_PATH, "assets")
 #  - Container definition for MaBoSS Building Block
 CONTAINER_NAME = "maboss.sif"
-MABOSS_CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+if CONTAINER_ENGINE == "SINGULARITY":
+    MABOSS_CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+    CONTAINER_OPTIONS = "[unassigned]"
+elif CONTAINER_ENGINE == "UDOCKER":
+    MABOSS_CONTAINER = CONTAINER_NAME.split(".")[0]
+    home_directory = os.environ["HOME"]
+    CONTAINER_OPTIONS = "-v " + home_directory + ":" + home_directory + " --rm"
+else:
+    raise Exception("UNSUPPORTED CONTAINER ENGINE: %s (must be SINGULARITY or UDOCKER)" % CONTAINER_ENGINE)

MaBoSS/src/MaBoSS_BB/main.py

@@ -10,7 +10,9 @@
 from permedcoe import TMPDIR
 
 # Import single container and assets definitions
+from MaBoSS_BB.definitions import CONTAINER_ENGINE
 from MaBoSS_BB.definitions import MABOSS_CONTAINER
+from MaBoSS_BB.definitions import CONTAINER_OPTIONS
 from MaBoSS_BB.definitions import ASSETS_PATH
 from MaBoSS_BB.definitions import COMPUTING_UNITS
 
@@ -20,7 +22,7 @@
 
 
 @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=MABOSS_CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=MABOSS_CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=MABOSS_BINARY)
 @task(data_folder=DIRECTORY_IN, ko_file=FILE_OUT)
 def MaBoSS_analysis(
@@ -38,7 +40,7 @@ def MaBoSS_analysis(
 
 
 @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=MABOSS_CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=MABOSS_CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=MABOSS_SENSITIVIY_ANALYSIS_BINARY)
 @task(
     model_folder=DIRECTORY_IN,

PhysiBoSS/src/PhysiBoSS_BB/definitions.py

@@ -4,10 +4,19 @@
 
 # Do not change this line
 BB_SOURCE_PATH=os.path.dirname(os.path.abspath(__file__))
+CONTAINER_ENGINE = os.environ["CONTAINER_ENGINE"]
 
 # Update the following lines:
 #  - Assets folder within the Building Block
 ASSETS_PATH = os.path.join(BB_SOURCE_PATH, "assets")
 #  - Container definition for Meta Analysis Building Block
 CONTAINER_NAME = "physicell_covid19.sif"
-CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+if CONTAINER_ENGINE == "SINGULARITY":
+    CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+    CONTAINER_OPTIONS = "[unassigned]"
+elif CONTAINER_ENGINE == "UDOCKER":
+    CONTAINER = CONTAINER_NAME.split(".")[0]
+    home_directory = os.environ["HOME"]
+    CONTAINER_OPTIONS = "-v " + home_directory + ":" + home_directory + " --rm"
+else:
+    raise Exception("UNSUPPORTED CONTAINER ENGINE: %s (must be SINGULARITY or UDOCKER)" % CONTAINER_ENGINE)

PhysiBoSS/src/PhysiBoSS_BB/main.py

@@ -11,8 +11,10 @@
 from permedcoe import TMPDIR
 
 # Import single container and assets definitions
-from PhysiBoSS_BB.definitions import CONTAINER
 from PhysiBoSS_BB.definitions import ASSETS_PATH
+from PhysiBoSS_BB.definitions import CONTAINER_ENGINE
+from PhysiBoSS_BB.definitions import CONTAINER
+from PhysiBoSS_BB.definitions import CONTAINER_OPTIONS
 from PhysiBoSS_BB.definitions import COMPUTING_UNITS
 
 # Globals# Globals
@@ -21,7 +23,7 @@
 PHYSIBOSS_ANALYSE_REPLICATES_BINARY = os.path.join(ASSETS_PATH, "PhysiBoSS_analyse_replicates.sh")
 
 @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=PHYSIBOSS_MODEL_BINARY)
 @task(
     model_dir=DIRECTORY_IN,
@@ -86,7 +88,7 @@ def physiboss_analyse_replicates(
 
 
 @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=PHYSIBOSS_BINARY)
 @task(
     bnd_file=FILE_IN,

meta_analysis/src/meta_analysis_BB/definitions.py

@@ -4,10 +4,20 @@
 
 # Do not change this line
 BB_SOURCE_PATH=os.path.dirname(os.path.abspath(__file__))
+CONTAINER_ENGINE = os.environ["CONTAINER_ENGINE"]
 
 # Update the following lines:
 #  - Assets folder within the Building Block
 ASSETS_PATH = os.path.join(BB_SOURCE_PATH, "assets")
 #  - Container definition for Meta Analysis Building Block
 CONTAINER_NAME = "meta_analysis.sif"
-CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+if CONTAINER_ENGINE == "SINGULARITY":
+    CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+    CONTAINER_OPTIONS = "[unassigned]"
+elif CONTAINER_ENGINE == "UDOCKER":
+    CONTAINER = CONTAINER_NAME.split(".")[0]
+    home_directory = os.environ["HOME"]
+    CONTAINER_OPTIONS = "-v " + home_directory + ":" + home_directory + " --rm"
+else:
+    raise Exception("UNSUPPORTED CONTAINER ENGINE: %s (must be SINGULARITY or UDOCKER)" % CONTAINER_ENGINE)
+

meta_analysis/src/meta_analysis_BB/main.py

@@ -10,16 +10,18 @@
 from permedcoe import TMPDIR
 
 # Import single container and assets definitions
-from meta_analysis_BB.definitions import CONTAINER
 from meta_analysis_BB.definitions import ASSETS_PATH
+from meta_analysis_BB.definitions import CONTAINER_ENGINE
+from meta_analysis_BB.definitions import CONTAINER
+from meta_analysis_BB.definitions import CONTAINER_OPTIONS
 from meta_analysis_BB.definitions import COMPUTING_UNITS
 
 # Globals
 META_ANALYSIS_BINARY = os.path.join(ASSETS_PATH, "meta_analysis.sh")
 
 
 # @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=META_ANALYSIS_BINARY)
 @task(meta_file=FILE_IN,
       out_dir=DIRECTORY_IN,

personalize_patient/src/personalize_patient_BB/definitions.py

@@ -4,10 +4,19 @@
 
 # Do not change this line
 BB_SOURCE_PATH=os.path.dirname(os.path.abspath(__file__))
+CONTAINER_ENGINE = os.environ["CONTAINER_ENGINE"]
 
 # Update the following lines:
 #  - Assets folder within the Building Block
 ASSETS_PATH = os.path.join(BB_SOURCE_PATH, "assets")
 #  - Container definition for Personalize Patient Building Block
 CONTAINER_NAME = "physicell_covid19.sif"
-CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+if CONTAINER_ENGINE == "SINGULARITY":
+    CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+    CONTAINER_OPTIONS = "[unassigned]"
+elif CONTAINER_ENGINE == "UDOCKER":
+    CONTAINER = CONTAINER_NAME.split(".")[0]
+    home_directory = os.environ["HOME"]
+    CONTAINER_OPTIONS = "-v " + home_directory + ":" + home_directory + " --rm"
+else:
+    raise Exception("UNSUPPORTED CONTAINER ENGINE: %s (must be SINGULARITY or UDOCKER)" % CONTAINER_ENGINE)

personalize_patient/src/personalize_patient_BB/main.py

@@ -10,8 +10,10 @@
 from permedcoe import TMPDIR
 
 # Import single container and assets definitions
-from personalize_patient_BB.definitions import CONTAINER
 from personalize_patient_BB.definitions import ASSETS_PATH
+from personalize_patient_BB.definitions import CONTAINER_ENGINE
+from personalize_patient_BB.definitions import CONTAINER
+from personalize_patient_BB.definitions import CONTAINER_OPTIONS
 from personalize_patient_BB.definitions import COMPUTING_UNITS
 
 # Globals
@@ -20,7 +22,7 @@
 
 
 # @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=PERSONALIZE_PATIENT_BINARY)
 @task(norm_data=FILE_IN, cells=FILE_IN, model_output_dir=DIRECTORY_OUT, personalized_result=FILE_OUT, ko=FILE_IN)
 def personalize_patient(tmpdir=TMPDIR,
@@ -56,7 +58,7 @@ def personalize_patient(tmpdir=TMPDIR,
     pass
 
 
-@container(engine="SINGULARITY", image=CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=PERSONALIZE_CELLLINE_BINARY)
 @task(expression_data=FILE_IN, cnv_data=FILE_IN, mutation_data=FILE_IN, model_bnd=FILE_IN, model_cfg=FILE_IN, model_output_dir=DIRECTORY_OUT)
 def personalize_patient_cellline(tmpdir=TMPDIR,

single_cell_processing/src/single_cell_processing_BB/definitions.py

@@ -4,10 +4,19 @@
 
 # Do not change this line
 BB_SOURCE_PATH=os.path.dirname(os.path.abspath(__file__))
+CONTAINER_ENGINE = os.environ["CONTAINER_ENGINE"]
 
 # Update the following lines:
 #  - Assets folder within the Building Block
 ASSETS_PATH = os.path.join(BB_SOURCE_PATH, "assets")
 #  - Container definition for Meta Analysis Building Block
 CONTAINER_NAME = "single_cell.sif"
-CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+if CONTAINER_ENGINE == "SINGULARITY":
+    CONTAINER = os.path.join(CONTAINER_PATH, CONTAINER_NAME)
+    CONTAINER_OPTIONS = "[unassigned]"
+elif CONTAINER_ENGINE == "UDOCKER":
+    CONTAINER = CONTAINER_NAME.split(".")[0]
+    home_directory = os.environ["HOME"]
+    CONTAINER_OPTIONS = "-v " + home_directory + ":" + home_directory + " --rm"
+else:
+    raise Exception("UNSUPPORTED CONTAINER ENGINE: %s (must be SINGULARITY or UDOCKER)" % CONTAINER_ENGINE)

single_cell_processing/src/single_cell_processing_BB/main.py

@@ -10,16 +10,18 @@
 from permedcoe import TMPDIR
 
 # Import single container and assets definitions
-from single_cell_processing_BB.definitions import CONTAINER
 from single_cell_processing_BB.definitions import ASSETS_PATH
+from single_cell_processing_BB.definitions import CONTAINER_ENGINE
+from single_cell_processing_BB.definitions import CONTAINER
+from single_cell_processing_BB.definitions import CONTAINER_OPTIONS
 from single_cell_processing_BB.definitions import COMPUTING_UNITS
 
 # Globals
 SINGLE_CELL_PROCESSING_BINARY = os.path.join(ASSETS_PATH, "single_cell_processing_individual.sh")
 
 
 @constraint(computing_units=COMPUTING_UNITS)
-@container(engine="SINGULARITY", image=CONTAINER)
+@container(engine=CONTAINER_ENGINE, image=CONTAINER, options=CONTAINER_OPTIONS)
 @binary(binary=SINGLE_CELL_PROCESSING_BINARY)
 @task(
     p_file=FILE_IN,