├── .gitignore ├── .travis.yml ├── LICENSE ├── README.rst ├── docs ├── Makefile ├── conf.py ├── index.rst └── make.bat ├── examples ├── .gitignore └── Snakefile ├── install.sh ├── requirements.txt ├── setup.cfg ├── setup.py ├── smbl ├── __init__.py ├── fasta │ ├── __init__.py │ ├── fasta.snake │ └── fastafile.py ├── include_all.snake ├── messages │ └── __init__.py ├── prog │ ├── __init__.py │ └── plugins │ │ ├── __init__.py │ │ ├── _program.py │ │ ├── art.py │ │ ├── bcftools.py │ │ ├── bfast.py │ │ ├── bowtie.py │ │ ├── bwa.py │ │ ├── cmake.py │ │ ├── curesim.py │ │ ├── deez.py │ │ ├── deprec │ │ └── gmap_gsnap.py │ │ ├── drfast.py │ │ ├── dwgsim.py │ │ ├── freec.py │ │ ├── gem.py │ │ ├── gnuplot.py │ │ ├── htslib.py │ │ ├── kallisto.py │ │ ├── last.py │ │ ├── mrfast.py │ │ ├── mrsfast.py │ │ ├── pbsim.py │ │ ├── perm.py │ │ ├── picard.py │ │ ├── sambamba.py │ │ ├── samtools.py │ │ ├── seqan.py │ │ ├── sirfast.py │ │ ├── storm.py │ │ ├── twobittofa.py │ │ ├── wgsim.py │ │ └── xs.py └── utils │ ├── __init__.py │ ├── clean.py │ ├── platforms.py │ ├── rule.py │ └── shell.py ├── tests ├── Snakefile.all_compatible_programs ├── Snakefile.all_fastas ├── Snakefile.all_programs ├── Snakefile.own_fasta ├── pytest_plugins.py ├── test_pytest_plugin.sh ├── tests_examples.sh ├── tests_fa.sh ├── tests_mt.sh └── tests_st.sh └── upload_pypi.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/karel-brinda/smbl/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/karel-brinda/smbl/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/karel-brinda/smbl/HEAD/LICENSE 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