diff --git a/__init__.py b/__init__.py index e69de29b..17653e01 100644 --- a/__init__.py +++ b/__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. +# diff --git a/setup.py b/setup.py index a897fa45..4b82d26e 100644 --- a/setup.py +++ b/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 diff --git a/src/toil_scripts/__init__.py b/src/toil_scripts/__init__.py index 4ecdf424..06313a6d 100644 --- a/src/toil_scripts/__init__.py +++ b/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__) diff --git a/src/toil_scripts/adam_gatk_pipeline/__init__.py b/src/toil_scripts/adam_gatk_pipeline/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/adam_gatk_pipeline/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/adam_gatk_pipeline/align_and_call.py b/src/toil_scripts/adam_gatk_pipeline/align_and_call.py index bebe20bc..e90787f9 100644 --- a/src/toil_scripts/adam_gatk_pipeline/align_and_call.py +++ b/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 fnothaft@berkeley.edu -@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. diff --git a/src/toil_scripts/adam_pipeline/__init__.py b/src/toil_scripts/adam_pipeline/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/adam_pipeline/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/adam_pipeline/adam_preprocessing.py b/src/toil_scripts/adam_pipeline/adam_preprocessing.py index 1681a40c..64c10089 100644 --- a/src/toil_scripts/adam_pipeline/adam_preprocessing.py +++ b/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, almussel@ucsc.edu -@author Frank Austin Nothaft, fnothaft@berkeley.edu - Please see the README.md in the same directory Toil pipeline for ADAM preprocessing diff --git a/src/toil_scripts/adam_uberscript/README.md b/src/toil_scripts/adam_uberscript/README.md index 0f4c87bc..219a0795 100644 --- a/src/toil_scripts/adam_uberscript/README.md +++ b/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=$PYTHONPATH:~/toil-scripts/src python -m toil_scripts.adam_uberscript.adam_uberscript launch-pipeline -c -j -B -m -s ` - Launch Metrics: - `PYTHONPATH=$PYTHONPATH:~/toil-scripts/src python -m toil_scripts.adam_uberscript.adam_uberscript launch-metrics -c "" -j --namespace $CGCLOUD_NAMESPACE -t r3.8xlarge` \ No newline at end of file + `PYTHONPATH=$PYTHONPATH:~/toil-scripts/src python -m toil_scripts.adam_uberscript.adam_uberscript launch-metrics -c "" -j --namespace $CGCLOUD_NAMESPACE -t r3.8xlarge` diff --git a/src/toil_scripts/adam_uberscript/__init__.py b/src/toil_scripts/adam_uberscript/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/adam_uberscript/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/adam_uberscript/adam_uberscript.py b/src/toil_scripts/adam_uberscript/adam_uberscript.py index d4cf7ae3..af079c6e 100644 --- a/src/toil_scripts/adam_uberscript/adam_uberscript.py +++ b/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 diff --git a/src/toil_scripts/adam_uberscript/automated_scaling.py b/src/toil_scripts/adam_uberscript/automated_scaling.py index aa6a5bfa..829d1661 100644 --- a/src/toil_scripts/adam_uberscript/automated_scaling.py +++ b/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 diff --git a/src/toil_scripts/adam_uberscript/boto_lib.py b/src/toil_scripts/adam_uberscript/boto_lib.py index a7d32b26..b67cbed8 100644 --- a/src/toil_scripts/adam_uberscript/boto_lib.py +++ b/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) \ No newline at end of file + cw.put_metric_alarm(alarm) diff --git a/src/toil_scripts/adam_uberscript/hg19.config b/src/toil_scripts/adam_uberscript/hg19.config index a5d88739..fd1cbaa8 100644 --- a/src/toil_scripts/adam_uberscript/hg19.config +++ b/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. \ No newline at end of file +memory: 225 # Amount of available memory on each worker node. diff --git a/src/toil_scripts/batch_alignment/README.md b/src/toil_scripts/batch_alignment/README.md index 1b9517e5..cbfbb89f 100644 --- a/src/toil_scripts/batch_alignment/README.md +++ b/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` - \ No newline at end of file + diff --git a/src/toil_scripts/batch_alignment/__init__.py b/src/toil_scripts/batch_alignment/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/batch_alignment/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/batch_alignment/bwa_alignment.py b/src/toil_scripts/batch_alignment/bwa_alignment.py index 55bd703d..c1c5b49a 100644 --- a/src/toil_scripts/batch_alignment/bwa_alignment.py +++ b/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 diff --git a/src/toil_scripts/batch_alignment/old_alignment_script/__init__.py b/src/toil_scripts/batch_alignment/old_alignment_script/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/batch_alignment/old_alignment_script/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/batch_alignment/old_alignment_script/batch_align.py b/src/toil_scripts/batch_alignment/old_alignment_script/batch_align.py index 67ee6b41..2b60ada6 100644 --- a/src/toil_scripts/batch_alignment/old_alignment_script/batch_align.py +++ b/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 """ diff --git a/src/toil_scripts/batch_alignment/test/__init__.py b/src/toil_scripts/batch_alignment/test/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/batch_alignment/test/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/batch_alignment/test/test_bwa_alignment.py b/src/toil_scripts/batch_alignment/test/test_bwa_alignment.py index 0458926a..8dd23ffc 100644 --- a/src/toil_scripts/batch_alignment/test/test_bwa_alignment.py +++ b/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 diff --git a/src/toil_scripts/exome_variant_pipeline/__init__.py b/src/toil_scripts/exome_variant_pipeline/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/exome_variant_pipeline/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/exome_variant_pipeline/exome_variant_pipeline.py b/src/toil_scripts/exome_variant_pipeline/exome_variant_pipeline.py index 159b11a2..57503067 100644 --- a/src/toil_scripts/exome_variant_pipeline/exome_variant_pipeline.py +++ b/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 diff --git a/src/toil_scripts/exome_variant_pipeline/test/__init__.py b/src/toil_scripts/exome_variant_pipeline/test/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/exome_variant_pipeline/test/__init__.py +++ b/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. +# diff --git a/src/toil_scripts/exome_variant_pipeline/test/test_exome.py b/src/toil_scripts/exome_variant_pipeline/test/test_exome.py index be13defc..37202f92 100644 --- a/src/toil_scripts/exome_variant_pipeline/test/test_exome.py +++ b/src/toil_scripts/exome_variant_pipeline/test/test_exome.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 shutil import subprocess diff --git a/src/toil_scripts/gatk_germline/__init__.py b/src/toil_scripts/gatk_germline/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/gatk_germline/__init__.py +++ b/src/toil_scripts/gatk_germline/__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. +# diff --git a/src/toil_scripts/gatk_germline/germline.py b/src/toil_scripts/gatk_germline/germline.py index 1bbc6f08..31df4aec 100644 --- a/src/toil_scripts/gatk_germline/germline.py +++ b/src/toil_scripts/gatk_germline/germline.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 """ diff --git a/src/toil_scripts/gatk_processing/__init__.py b/src/toil_scripts/gatk_processing/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/gatk_processing/__init__.py +++ b/src/toil_scripts/gatk_processing/__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. +# diff --git a/src/toil_scripts/gatk_processing/gatk_preprocessing.py b/src/toil_scripts/gatk_processing/gatk_preprocessing.py old mode 100755 new mode 100644 index 3df4701b..12155e7a --- a/src/toil_scripts/gatk_processing/gatk_preprocessing.py +++ b/src/toil_scripts/gatk_processing/gatk_preprocessing.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 Jacob Pfeil -@data 01/13/2016 +""" Toil pipeline for processing bam files for GATK halpotype calling 1 = download shared data diff --git a/src/toil_scripts/general_documentation/tcga_data_on_podk.md b/src/toil_scripts/general_documentation/tcga_data_on_podk.md index 16e17a65..a5257e98 100644 --- a/src/toil_scripts/general_documentation/tcga_data_on_podk.md +++ b/src/toil_scripts/general_documentation/tcga_data_on_podk.md @@ -70,4 +70,4 @@ For example: `ssh USER@podk-1-2`. I generally run my pipelines in a screen, so Now, make sure your **venv** is active and **LD_LIBRARY_PATH** is set. If everything has been setup properly you should be able to type `time ./launch.sh` to kick off the pipeline. -Save any stack traces to send to the author if you encounter issues. \ No newline at end of file +Save any stack traces to send to the author if you encounter issues. diff --git a/src/toil_scripts/lib/__init__.py b/src/toil_scripts/lib/__init__.py index dccd7e71..8813013e 100644 --- a/src/toil_scripts/lib/__init__.py +++ b/src/toil_scripts/lib/__init__.py @@ -1,7 +1,22 @@ +# +# 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 tempfile - def flatten(x): """ Flattens a nested array into a single list diff --git a/src/toil_scripts/lib/files.py b/src/toil_scripts/lib/files.py index 1e9d2954..9c410d5c 100644 --- a/src/toil_scripts/lib/files.py +++ b/src/toil_scripts/lib/files.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. +# from contextlib import closing import os import tarfile diff --git a/src/toil_scripts/lib/jobs.py b/src/toil_scripts/lib/jobs.py index f9637bc9..335d870a 100644 --- a/src/toil_scripts/lib/jobs.py +++ b/src/toil_scripts/lib/jobs.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. +# from toil_scripts.lib import partitions diff --git a/src/toil_scripts/lib/programs.py b/src/toil_scripts/lib/programs.py index bb03a416..d639394c 100644 --- a/src/toil_scripts/lib/programs.py +++ b/src/toil_scripts/lib/programs.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 logging diff --git a/src/toil_scripts/lib/test/__init__.py b/src/toil_scripts/lib/test/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/lib/test/__init__.py +++ b/src/toil_scripts/lib/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. +# diff --git a/src/toil_scripts/lib/test/test_files.py b/src/toil_scripts/lib/test/test_files.py index 929cc498..4fb18ca3 100644 --- a/src/toil_scripts/lib/test/test_files.py +++ b/src/toil_scripts/lib/test/test_files.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 tarfile from toil.job import Job diff --git a/src/toil_scripts/lib/test/test_jobs.py b/src/toil_scripts/lib/test/test_jobs.py index c06653a6..dfb5abf0 100644 --- a/src/toil_scripts/lib/test/test_jobs.py +++ b/src/toil_scripts/lib/test/test_jobs.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 from toil.job import Job from toil_scripts.lib import get_work_directory diff --git a/src/toil_scripts/lib/test/test_lib.py b/src/toil_scripts/lib/test/test_lib.py index 9d1acf45..9429c80f 100644 --- a/src/toil_scripts/lib/test/test_lib.py +++ b/src/toil_scripts/lib/test/test_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. +# def test_flatten(): from toil_scripts.lib import flatten x = [(1, 2), (3, 4, (5, 6))] diff --git a/src/toil_scripts/lib/test/test_programs.py b/src/toil_scripts/lib/test/test_programs.py index 3c75ac4f..db2004ad 100644 --- a/src/toil_scripts/lib/test/test_programs.py +++ b/src/toil_scripts/lib/test/test_programs.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 diff --git a/src/toil_scripts/lib/test/test_urls.py b/src/toil_scripts/lib/test/test_urls.py index 2b394d87..21ae2138 100644 --- a/src/toil_scripts/lib/test/test_urls.py +++ b/src/toil_scripts/lib/test/test_urls.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 filecmp diff --git a/src/toil_scripts/lib/urls.py b/src/toil_scripts/lib/urls.py index b2043bd9..9b5d2682 100644 --- a/src/toil_scripts/lib/urls.py +++ b/src/toil_scripts/lib/urls.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 base64 import glob import hashlib diff --git a/src/toil_scripts/rnaseq_cgl/__init__.py b/src/toil_scripts/rnaseq_cgl/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/rnaseq_cgl/__init__.py +++ b/src/toil_scripts/rnaseq_cgl/__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. +# diff --git a/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py b/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py index edc73b0e..e89fedc1 100644 --- a/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py +++ b/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_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 from __future__ import print_function diff --git a/src/toil_scripts/rnaseq_cgl/test/__init__.py b/src/toil_scripts/rnaseq_cgl/test/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/rnaseq_cgl/test/__init__.py +++ b/src/toil_scripts/rnaseq_cgl/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. +# diff --git a/src/toil_scripts/rnaseq_cgl/test/test_rnaseq_cgl.py b/src/toil_scripts/rnaseq_cgl/test/test_rnaseq_cgl.py index 6471dac3..52f1035c 100644 --- a/src/toil_scripts/rnaseq_cgl/test/test_rnaseq_cgl.py +++ b/src/toil_scripts/rnaseq_cgl/test/test_rnaseq_cgl.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 shutil import subprocess diff --git a/src/toil_scripts/rnaseq_unc/README.md b/src/toil_scripts/rnaseq_unc/README.md index 312aa800..14bab5a5 100644 --- a/src/toil_scripts/rnaseq_unc/README.md +++ b/src/toil_scripts/rnaseq_unc/README.md @@ -144,4 +144,4 @@ If encryption keys of any type will be used, they must be **exactly** 32-byte ke This pipeline aligns data to the HG19 human reference genome before performing RNA-seq analysis. If you want to align to a different genome then you will need to look at the help menu `python rnaseq_unc_pipeline.py -h` to see all of the different inputs that you will need to change. Support is not offered if you would like to use a different -reference genome. Our group plans on developing a new RNA-seq pipeline for HG38 that uses STAR+RSEM and Kallisto. \ No newline at end of file +reference genome. Our group plans on developing a new RNA-seq pipeline for HG38 that uses STAR+RSEM and Kallisto. diff --git a/src/toil_scripts/rnaseq_unc/__init__.py b/src/toil_scripts/rnaseq_unc/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/rnaseq_unc/__init__.py +++ b/src/toil_scripts/rnaseq_unc/__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. +# diff --git a/src/toil_scripts/rnaseq_unc/rnaseq_unc_pipeline.py b/src/toil_scripts/rnaseq_unc/rnaseq_unc_pipeline.py index 5aa7a04a..e4a14e64 100644 --- a/src/toil_scripts/rnaseq_unc/rnaseq_unc_pipeline.py +++ b/src/toil_scripts/rnaseq_unc/rnaseq_unc_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 """ UNC Best Practice RNA-Seq Pipeline diff --git a/src/toil_scripts/rnaseq_unc/rnaseq_unc_tcga_versions.py b/src/toil_scripts/rnaseq_unc/rnaseq_unc_tcga_versions.py index 65814277..c24da1ac 100644 --- a/src/toil_scripts/rnaseq_unc/rnaseq_unc_tcga_versions.py +++ b/src/toil_scripts/rnaseq_unc/rnaseq_unc_tcga_versions.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 """ UNC Best Practice RNA-Seq Pipeline diff --git a/src/toil_scripts/rnaseq_unc/unc_config.csv b/src/toil_scripts/rnaseq_unc/unc_config.csv index 552bba25..228aa9bd 100644 --- a/src/toil_scripts/rnaseq_unc/unc_config.csv +++ b/src/toil_scripts/rnaseq_unc/unc_config.csv @@ -1 +1 @@ -HS1801,https://s3-us-west-2.amazonaws.com/cgl-driver-projects-encrypted/treehouse/rnaseq-neuroblastoma/HS1801.tar \ No newline at end of file +HS1801,https://s3-us-west-2.amazonaws.com/cgl-driver-projects-encrypted/treehouse/rnaseq-neuroblastoma/HS1801.tar diff --git a/src/toil_scripts/spark_utils/__init__.py b/src/toil_scripts/spark_utils/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/spark_utils/__init__.py +++ b/src/toil_scripts/spark_utils/__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. +# diff --git a/src/toil_scripts/spark_utils/spawn_cluster.py b/src/toil_scripts/spark_utils/spawn_cluster.py index 8c0a6692..83ed065c 100644 --- a/src/toil_scripts/spark_utils/spawn_cluster.py +++ b/src/toil_scripts/spark_utils/spawn_cluster.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. +# + """ Spawns a Spark cluster backed by HDFS. - -@author Audrey Musselman-Brown, almussel@ucsc.edu -@author Frank Austin Nothaft, fnothaft@berkeley.edu """ import logging diff --git a/src/toil_scripts/spladder_pipeline/__init__.py b/src/toil_scripts/spladder_pipeline/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/spladder_pipeline/__init__.py +++ b/src/toil_scripts/spladder_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. +# diff --git a/src/toil_scripts/spladder_pipeline/example_config.txt b/src/toil_scripts/spladder_pipeline/example_config.txt index c47dcdbc..76d0da9c 100644 --- a/src/toil_scripts/spladder_pipeline/example_config.txt +++ b/src/toil_scripts/spladder_pipeline/example_config.txt @@ -1,2 +1,2 @@ UUID1,http://www.url.com/sample1 -UUID2,http://www.url.com/sample2 \ No newline at end of file +UUID2,http://www.url.com/sample2 diff --git a/src/toil_scripts/spladder_pipeline/spladder_pipeline.py b/src/toil_scripts/spladder_pipeline/spladder_pipeline.py index 32435fad..5d3081b4 100644 --- a/src/toil_scripts/spladder_pipeline/spladder_pipeline.py +++ b/src/toil_scripts/spladder_pipeline/spladder_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 """ UCSC Computational Genomics Lab Spladder Pipeline diff --git a/src/toil_scripts/tools/QC.py b/src/toil_scripts/tools/QC.py index c4a05413..61d5f6e0 100644 --- a/src/toil_scripts/tools/QC.py +++ b/src/toil_scripts/tools/QC.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 from toil_scripts.lib.files import tarball_files diff --git a/src/toil_scripts/tools/__init__.py b/src/toil_scripts/tools/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/tools/__init__.py +++ b/src/toil_scripts/tools/__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. +# diff --git a/src/toil_scripts/tools/aligners.py b/src/toil_scripts/tools/aligners.py index c4e9fd6e..40c6a8d4 100644 --- a/src/toil_scripts/tools/aligners.py +++ b/src/toil_scripts/tools/aligners.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 diff --git a/src/toil_scripts/tools/preprocessing.py b/src/toil_scripts/tools/preprocessing.py index 2797c626..4706c75c 100644 --- a/src/toil_scripts/tools/preprocessing.py +++ b/src/toil_scripts/tools/preprocessing.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 from toil_scripts.lib import require diff --git a/src/toil_scripts/tools/quantifiers.py b/src/toil_scripts/tools/quantifiers.py index b1c5e295..eff1b91d 100644 --- a/src/toil_scripts/tools/quantifiers.py +++ b/src/toil_scripts/tools/quantifiers.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 diff --git a/src/toil_scripts/transfer_gtex_to_s3/launch.sh b/src/toil_scripts/transfer_gtex_to_s3/launch.sh index fbfe5ad8..0f2e6094 100755 --- a/src/toil_scripts/transfer_gtex_to_s3/launch.sh +++ b/src/toil_scripts/transfer_gtex_to_s3/launch.sh @@ -12,4 +12,4 @@ python transfer_gtex_to_s3.py \ --s3 gtex-data \ --workDir /var/lib/toil \ --retryCount 2 \ -#--restart \ No newline at end of file +#--restart diff --git a/src/toil_scripts/transfer_gtex_to_s3/launch_mesos.sh b/src/toil_scripts/transfer_gtex_to_s3/launch_mesos.sh index 6171ae12..77b90e4e 100755 --- a/src/toil_scripts/transfer_gtex_to_s3/launch_mesos.sh +++ b/src/toil_scripts/transfer_gtex_to_s3/launch_mesos.sh @@ -13,4 +13,4 @@ aws:us-west-2:gtex-transfer-run-1 \ --mesosMaster mesos-master:5050 \ --workDir /var/lib/toil \ --retryCount 2 \ -#--restart \ No newline at end of file +#--restart diff --git a/src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.py b/src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.py index 196bb8f9..cfd7db42 100644 --- a/src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.py +++ b/src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.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 """ Toil script to move TCGA data into an S3 bucket. @@ -198,4 +213,4 @@ def main(): Job.Runner.startToil(Job.wrapJobFn(start_batch, inputs), args) if __name__ == '__main__': - main() \ No newline at end of file + main() diff --git a/src/toil_scripts/transfer_tcga_to_s3/__init__.py b/src/toil_scripts/transfer_tcga_to_s3/__init__.py index e69de29b..444feaf8 100644 --- a/src/toil_scripts/transfer_tcga_to_s3/__init__.py +++ b/src/toil_scripts/transfer_tcga_to_s3/__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. +# diff --git a/src/toil_scripts/transfer_tcga_to_s3/launch_transfer.sh b/src/toil_scripts/transfer_tcga_to_s3/launch_transfer.sh index d6ed21a8..5fa16a46 100755 --- a/src/toil_scripts/transfer_tcga_to_s3/launch_transfer.sh +++ b/src/toil_scripts/transfer_tcga_to_s3/launch_transfer.sh @@ -12,4 +12,4 @@ python -m toil_scripts.transfer_tcga_to_s3.transfer_tcga_to_s3 \ --s3 tcga-data-cgl-recompute \ --workDir /var/lib/toil \ --retryCount 2 \ -#--restart \ No newline at end of file +#--restart diff --git a/src/toil_scripts/transfer_tcga_to_s3/transfer_tcga_to_s3.py b/src/toil_scripts/transfer_tcga_to_s3/transfer_tcga_to_s3.py index a72c6527..79b933f1 100644 --- a/src/toil_scripts/transfer_tcga_to_s3/transfer_tcga_to_s3.py +++ b/src/toil_scripts/transfer_tcga_to_s3/transfer_tcga_to_s3.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 """ Toil script to move TCGA data into an S3 bucket. @@ -180,4 +195,4 @@ def main(): if __name__ == '__main__': - main() \ No newline at end of file + main() diff --git a/version.py b/version.py index 3106a0d8..75541458 100644 --- a/version.py +++ b/version.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. @@ -11,5 +12,6 @@ # 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. +# version = '2.0a5'