mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
a850a47419
Fix `pysam.index()` calls which now use samtools 1.16 where `samtools index input output` doesn't work any more if `output` is the path of an already existing file, but `samtools index -o output input` works fine. Also: - Pre-create the (empty) index file for mock test datasets as a unit test reproducer of the above issue. - Fix `test_cram` unit test that wasn't checking the return value of `CRAM.set_index_file()`, which was in fact returning False because `test-data/2.cram` was not sorted (updated now).
71 lines
1.8 KiB
INI
71 lines
1.8 KiB
INI
[metadata]
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author = Galaxy Project and Community
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author_email = galaxy-committers@lists.galaxyproject.org
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classifiers =
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Development Status :: 5 - Production/Stable
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Environment :: Console
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Intended Audience :: Developers
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License :: OSI Approved :: Academic Free License (AFL)
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Natural Language :: English
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Operating System :: POSIX
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Programming Language :: Python :: 3
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Programming Language :: Python :: 3.7
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Programming Language :: Python :: 3.8
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Programming Language :: Python :: 3.9
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Programming Language :: Python :: 3.10
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Topic :: Software Development
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Topic :: Software Development :: Code Generators
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Topic :: Software Development :: Testing
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description = Galaxy datatype framework and datatypes
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keywords =
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Galaxy
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license = AFL
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license_files =
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LICENSE
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long_description = file: README.rst, HISTORY.rst
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long_description_content_type = text/x-rst
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name = galaxy-data
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url = https://github.com/galaxyproject/galaxy
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version = 22.5.0.dev0
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[options]
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include_package_data = True
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install_requires =
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galaxy-files
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galaxy-objectstore
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galaxy-util[template]
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alembic
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bdbag
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bx-python
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dnspython
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galaxy-sequence-utils
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h5py
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isa-rwval
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MarkupSafe
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mrcfile
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numpy
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parsley
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pycryptodome
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pydantic[email]
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pylibmagic
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python-magic
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pysam>=0.20
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rocrate
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social-auth-core[openidconnect]==4.0.3
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SQLAlchemy>=1.4.25,<2
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tifffile
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typing-extensions
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WebOb
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packages = find:
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python_requires = >=3.7
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[options.entry_points]
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console_scripts =
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galaxy-build-objects = galaxy.model.store.build_objects:main
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galaxy-load-objects = galaxy.model.store.load_objects:main
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galaxy-manage-db = galaxy.model.orm.scripts:manage_db
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[options.packages.find]
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exclude =
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tests*
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