├── .coveragerc ├── .gitignore ├── .travis.yml ├── CHANGES.txt ├── LICENSE ├── MANIFEST.in ├── README.md ├── biomaj ├── __init__.py ├── bank.py ├── mongo_connector.py ├── notify.py ├── options.py ├── process │ ├── __init__.py │ ├── metaprocess.py │ └── processfactory.py ├── schema_version.py ├── session.py └── workflow.py ├── config.yml ├── docs ├── Makefile ├── admin.rst ├── alu.properties ├── bank.rst ├── conf.py ├── docker-compose-advanced.yml ├── docker-compose.yml ├── examples.rst ├── global.advanced.properties ├── index.rst ├── make.bat ├── metaprocess.rst ├── notify.rst ├── options.rst ├── processfactory.rst ├── requirements.txt ├── session.rst └── workflow.rst ├── global.properties.example ├── requirements.txt ├── scripts ├── biomaj_add_property.py ├── biomaj_migrate_database.py └── influxdb_import.py ├── setup.cfg ├── setup.py ├── tests ├── alu_list_error.properties ├── bank │ ├── process │ │ └── test.sh │ ├── test.fasta.gz │ ├── test2.fasta │ └── test_100.txt ├── biomaj_tests.py ├── computed.properties ├── computed2.properties ├── computederror.properties ├── directhttp.properties ├── error.properties ├── global.properties ├── local.properties ├── locallist.properties ├── localprocess.properties ├── multi.properties ├── pdbaa.properties ├── sub1.properties ├── sub2.properties └── testhttp.properties └── tools ├── examples ├── alu.properties ├── body.jinja2 ├── global.properties ├── local.properties └── subject.jinja2 └── process ├── concat.sh ├── formatdb.sh ├── makeblastdb.sh └── scan.py /.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | source = biomaj 3 | 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/genouest/biomaj/HEAD/.gitignore -------------------------------------------------------------------------------- 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