[PACKAGES-12] Move toil-bdg to bdgenomics.packages.

Resolves #12.
bigdatagenomics · Aug 31, 2017 · 90330f7 · 90330f7
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commit 90330f7
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Showing 16 changed files with 11 additions and 12 deletions.
diff --git a/src/toil_bdg/__init__.py → bdgenomics/pipelines/__init__.py b/src/toil_bdg/__init__.py → bdgenomics/pipelines/__init__.py
diff --git a/src/toil_bdg/adam_pipeline/__init__.py → ...omics/pipelines/adam_pipeline/__init__.py b/src/toil_bdg/adam_pipeline/__init__.py → ...omics/pipelines/adam_pipeline/__init__.py
diff --git a/src/toil_bdg/adam_pipeline/preprocessing.py → .../pipelines/adam_pipeline/preprocessing.py b/src/toil_bdg/adam_pipeline/preprocessing.py → .../pipelines/adam_pipeline/preprocessing.py
diff --git a/src/toil_bdg/avocado_pipeline/__init__.py → ...cs/pipelines/avocado_pipeline/__init__.py b/src/toil_bdg/avocado_pipeline/__init__.py → ...cs/pipelines/avocado_pipeline/__init__.py
diff --git a/...l_bdg/avocado_pipeline/variant_calling.py → ...lines/avocado_pipeline/variant_calling.py b/...l_bdg/avocado_pipeline/variant_calling.py → ...lines/avocado_pipeline/variant_calling.py
diff --git a/src/toil_bdg/benchmarking/__init__.py → ...nomics/pipelines/benchmarking/__init__.py b/src/toil_bdg/benchmarking/__init__.py → ...nomics/pipelines/benchmarking/__init__.py
diff --git a/...g/benchmarking/gatk3_pipeline/__init__.py → ...s/benchmarking/gatk3_pipeline/__init__.py b/...g/benchmarking/gatk3_pipeline/__init__.py → ...s/benchmarking/gatk3_pipeline/__init__.py
diff --git a/...chmarking/gatk3_pipeline/preprocessing.py → ...chmarking/gatk3_pipeline/preprocessing.py b/...chmarking/gatk3_pipeline/preprocessing.py → ...chmarking/gatk3_pipeline/preprocessing.py
diff --git a/..._bdg/benchmarking/single_node/__init__.py → ...ines/benchmarking/single_node/__init__.py b/..._bdg/benchmarking/single_node/__init__.py → ...ines/benchmarking/single_node/__init__.py
diff --git a/...toil_bdg/benchmarking/single_node/bqsr.py → ...ipelines/benchmarking/single_node/bqsr.py b/...toil_bdg/benchmarking/single_node/bqsr.py → ...ipelines/benchmarking/single_node/bqsr.py
diff --git a/...il_bdg/benchmarking/single_node/mkdups.py → ...elines/benchmarking/single_node/mkdups.py b/...il_bdg/benchmarking/single_node/mkdups.py → ...elines/benchmarking/single_node/mkdups.py
diff --git a/...enchmarking/single_node/realign_indels.py → ...enchmarking/single_node/realign_indels.py b/...enchmarking/single_node/realign_indels.py → ...enchmarking/single_node/realign_indels.py
diff --git a/...toil_bdg/benchmarking/single_node/sort.py → ...ipelines/benchmarking/single_node/sort.py b/...toil_bdg/benchmarking/single_node/sort.py → ...ipelines/benchmarking/single_node/sort.py
diff --git a/src/toil_bdg/cannoli_pipeline/__init__.py → ...cs/pipelines/cannoli_pipeline/__init__.py b/src/toil_bdg/cannoli_pipeline/__init__.py → ...cs/pipelines/cannoli_pipeline/__init__.py
diff --git a/...oil_bdg/cannoli_pipeline/bwa_alignment.py → ...pelines/cannoli_pipeline/bwa_alignment.py b/...oil_bdg/cannoli_pipeline/bwa_alignment.py → ...pelines/cannoli_pipeline/bwa_alignment.py
diff --git a/setup.py b/setup.py
@@ -61,12 +61,12 @@ def check_provided(distribution, min_version, max_version=None, optional=False):
         return version
 
 
-toil_version = check_provided('toil', min_version='3.7.0a1.dev392', max_version='3.7.0a1.dev392')
+toil_version = check_provided('toil', min_version='3.7.0a1.dev392', max_version='3.10.0')
 check_provided('bd2k-python-lib', min_version='1.14a1.dev29' )
 check_provided('boto', min_version='2.38.0', optional=True)
 
 kwargs = dict(
-    name='toil-bdg',
+    name='bdgenomics.pipelines',
     version=version,
     description='A repository of genomic workflows developed by the UC Berkeley AMPLab and UCSC Computational Genomics lab that use Toil to run ADAM/BDG tools',
     author='UC Berkeley AMP Lab',
@@ -76,18 +76,17 @@ def check_provided(distribution, min_version, max_version=None, optional=False):
         'pyyaml==3.11'],
     tests_require=[
         'pytest==2.8.3'],
-    package_dir={'': 'src'},
-    packages=find_packages('src'),
     entry_points={
         'console_scripts': [
-            'toil-adam = toil_bdg.adam_pipeline.preprocessing:main',
-            'toil-avocado = toil_bdg.avocado_pipeline.variant_calling:main',
-            'toil-cannoli-bwa = toil_bdg.cannoli_pipeline.bwa_alignment:main',
-            'toil-bdg-gatk3-benchmark = toil_bdg.benchmarking.gatk3_pipeline.preprocessing:main',
-            'toil-bdg-mkdups-benchmark = toil_bdg.benchmarking.single_node.mkdups:main',
-            'toil-bdg-sort-benchmark = toil_bdg.benchmarking.single_node.sort:main',
-            'toil-bdg-ri-benchmark = toil_bdg.benchmarking.single_node.realign_indels:main',
-            'toil-bdg-bqsr-benchmark = toil_bdg.benchmarking.single_node.bqsr:main']})
+            'bdg-adam = bdgenomics.pipeline.adam_pipeline.preprocessing:main',
+            'bdg-avocado = bdgenomics.pipeline.avocado_pipeline.variant_calling:main',
+            'bdg-cannoli-bwa = bdgenomics.pipeline.cannoli_pipeline.bwa_alignment:main',
+            'bdg-gatk3-benchmark = bdgenomics.pipeline.benchmarking.gatk3_pipeline.preprocessing:main',
+            'bdg-mkdups-benchmark = bdgenomics.pipeline.benchmarking.single_node.mkdups:main',
+            'bdg-sort-benchmark = bdgenomics.pipeline.benchmarking.single_node.sort:main',
+            'bdg-ri-benchmark = bdgenomics.pipeline.benchmarking.single_node.realign_indels:main',
+            'bdg-bqsr-benchmark = bdgenomics.pipeline.benchmarking.single_node.bqsr:main']},
+    packages=find_packages())
 
 
 class PyTest(TestCommand):