Clean up source file headers (resolves #309, #310)

__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015–2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

setup.py

@@ -1,4 +1,5 @@
-# Copyright (C) 2015 UCSC Computational Genomics Lab
+#
+# Copyright 2015-2016, Regents of the University of California
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -11,6 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+#
 
 from __future__ import print_function
 

src/toil_scripts/__init__.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 import logging
 
 _log = logging.getLogger(__name__)

src/toil_scripts/adam_gatk_pipeline/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/adam_gatk_pipeline/align_and_call.py

@@ -1,8 +1,21 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 #!/usr/bin/env python2.7
-"""
-@author Frank Austin Nothaft [email protected]
-@date 12/30/2015
 
+"""
 Pipeline to go from FASTQ to VCF using both the ADAM+HaplotypeCaller pipeline
 as well as the GATK best practices pipeline.
 

src/toil_scripts/adam_pipeline/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/adam_pipeline/adam_preprocessing.py

@@ -1,10 +1,23 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 #!/usr/bin/env python2.7
+
 """
 UCSC Computational Genomics Lab ADAM/Spark pipeline
 
-@author Audrey Musselman-Brown, [email protected]
-@author Frank Austin Nothaft, [email protected]
-
 Please see the README.md in the same directory
 
 Toil pipeline for ADAM preprocessing

src/toil_scripts/adam_uberscript/README.md

@@ -40,4 +40,4 @@ This document assumes that all machines are run in a separate
     - Launch Pipeline:
         `PYTHONPATH=$PYTHONPATH:~/toil-scripts/src python -m toil_scripts.adam_uberscript.adam_uberscript launch-pipeline -c <cluster name> -j <jobstore> -B <data bucket> -m <memory per worker node> -s <spark cluster size including master>`
     - Launch Metrics:
-        `PYTHONPATH=$PYTHONPATH:~/toil-scripts/src python -m toil_scripts.adam_uberscript.adam_uberscript launch-metrics -c "<cluster name>" -j <jobstore> --namespace $CGCLOUD_NAMESPACE -t r3.8xlarge`
+        `PYTHONPATH=$PYTHONPATH:~/toil-scripts/src python -m toil_scripts.adam_uberscript.adam_uberscript launch-metrics -c "<cluster name>" -j <jobstore> --namespace $CGCLOUD_NAMESPACE -t r3.8xlarge`

src/toil_scripts/adam_uberscript/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/adam_uberscript/adam_uberscript.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 #!/usr/bin/env python2.7
 
 # Initialize logging before the remaining imports to prevent those imported modules from snatching that one shot at 

src/toil_scripts/adam_uberscript/automated_scaling.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 import sys
 import threading
 import time

src/toil_scripts/adam_uberscript/boto_lib.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 #!/usr/bin/env python2.7
 """
 Author: John Vivian
@@ -207,4 +222,4 @@ def apply_alarm_to_instance(instance_id, namespace='AWS/EC2', metric='CPUUtiliza
                                             threshold=threshold, period=period, evaluation_periods=evaluation_periods,
                                             dimensions={'InstanceId': [instance_id]},
                                             alarm_actions=['arn:aws:automate:{}:ec2:terminate'.format(region)])
-    cw.put_metric_alarm(alarm)
+    cw.put_metric_alarm(alarm)

src/toil_scripts/adam_uberscript/hg19.config

@@ -31,4 +31,4 @@ file-size: 100G           # Approximate input file size. Should be given as %d[T
                                   # for a 100 gigabyte file, use file_size: '100G'
 ssec:                     # (string) Path to Key File for SSE-C Encryption
 dir-suffix: /hg19         # Optional suffix to add to output directory names.
-memory: 225               # Amount of available memory on each worker node.
+memory: 225               # Amount of available memory on each worker node.

src/toil_scripts/batch_alignment/README.md

@@ -44,4 +44,4 @@ Due to PYTHONPATH issues, help can be found by typing:
 
 * `cd toil-scripts/src`
 * `python -m toil_scripts.batch_alignment.bwa_alignment --help`
-
+

src/toil_scripts/batch_alignment/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/batch_alignment/bwa_alignment.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 """
 UC Santa Cruz Computational Genomics Lab
 Updated: 4/21/16

src/toil_scripts/batch_alignment/old_alignment_script/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/batch_alignment/old_alignment_script/batch_align.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 #!/usr/bin/env python2.7
 # John Vivian
 """

src/toil_scripts/batch_alignment/test/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/batch_alignment/test/test_bwa_alignment.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 import os
 import subprocess
 import shutil

src/toil_scripts/exome_variant_pipeline/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

src/toil_scripts/exome_variant_pipeline/exome_variant_pipeline.py

@@ -1,3 +1,18 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 #!/usr/bin/env python2.7
 import argparse
 import multiprocessing

src/toil_scripts/exome_variant_pipeline/test/__init__.py

@@ -0,0 +1,15 @@
+#
+# Copyright 2015-2016, Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#