Resolwe-bio

================

Changed
-------
- Update ``resolwe`` requirement


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Changed
-------
- Decorate all tests that currently fail on Docker with ``skipDockerFailure``
- Require Resolwe's ``master`` git branch
- Put packaging tests in a separate Tox testing environment
- Rename DB user in test project
- Change PostgreSQL port in test project
- Add ROSE2 results parser
- Compute index for HISAT2 aligner on genome upload
- Updated Cuffquant/Cuffnorm tools
- Change ROSE2 enhancer rank plot labels
- Refactor processor syntax
- Move processes tests into ``processes`` subdirectory
- Split ``sample`` API endpoint to ``sample`` for annotated ``Samples``
and ``presample`` for unannotated ``Samples``
- Rename test project's data and upload directories to ``.test_data`` and
``.test_upload``
- Save fastq files to ``lists:basic:file`` field. Refactor related processors.
- Reference genome-index path when running aligners.
- Add pre-computed genome-index files when uploading reference fasta file.
- Include all necessary files for running the tests in source distribution
- Exclude tests from built/installed version of the package
- Move testing utilities from ``resolwe_bio.tests.processes.utils`` to
``resolwe_bio.utils.test``
- Update Cuffdiff processor inputs and results table parsing
- Refactor processes to use the updated ``resolwe.flow.executors.run`` command
- Refactor STAR aligner - export expressions as separate objects

Fixed
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- Make Tox configuration more robust to different developer environments
- Set ``required: false`` in processor input/output fields where necessary
- Add ``Sample``'s ``Data objects`` to ``Collection`` when ``Sample`` is added
- Fixed/renamed Cufflinks processor field names

Added
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- ``skipDockerFailure`` test decorator
- Expand documentation on running tests
- Use Travis CI to run the tests
- Add ``Sample`` model and corresponding viewset and filter
- Add docker-compose command for PostgreSQL
- API endpoint for adding ``Samples`` to ``Collections``
- HISAT2 aligner
- Use Git Large File Storage (LFS) for large test files
- Test for ``generate_samples`` django-admin command
- django-admin command: ``generate_diffexpr``


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Changed
-------
- Remove obsolete utilities superseded by resolwe-runtime-utils
- Require Resolwe 1.1.0

Fixed
-----
- Update sample descriptor schema
- Include all source files and supplementary package data in sdist

Added
-----
- ``flow_collection: sample`` to processes
- MACS14 processor
- Initial Tox configuration for running the tests
- Tox tests for ensuring high-quality Python packaging
- ROSE2 processor
- django-admin command: ``generate_samples``


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Changed
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- Renamed assertFileExist to assertFileExists
- Restructured processes folder hierarchy
- Removed re-require and hard-coded tools' paths

Fixed
-----
- Different line endings are correctly handled when opening gzipped files
- Fail gracefully if the field does not exist in assertFileExists
- Enabled processor tests (GO, Expression, Variant Calling)
- Enabled processor test (Upload reads with old Illumina QC encoding)
- Made Resolwe Bioinformatics work with Resolwe and Docker

Added
-----
- Import expressions from tranSMART
- Limma differential expression (tranSMART)
- VC filtering tool (Chemical mutagenesis)
- Additional analysis options to Abyss assembler
- API endpoint for Sample
- Initial documentation


===============
Process catalog
===============

Resolwe Bioinformatics includes over 100 processes. They
are organized in categories. The type tree will help process developers
with pipeline design. For process details browse process definitions.

.. toctree::
:maxdepth: 1

catalog-category
catalog-types
catalog-definitions