broadinstitute / viral-ngs / 4516

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WIP snakemake db refactor to accept cloud paths (#644)

* refactor snakemake rules to have more flexible DB paths

snakemake database paths now more flexible, and can accept cloud
pseudoprotocols (or local paths); addresses #639, #636,

* remove py34 from build matrix

* monkeypatch boto.connect_s3 for anonymous auth for testing

* adjustments for snakemake metagenomics tests

* hide conda install progress bar

* metagenomics file lists changed to reflect only necessary files

* added merged.dmp to taxonomy files

* add merged.dmp to test_diamond

* bump boto; metag db changes

* rearrange some dependencies now that we're dropping py34 from the build matrix

rearrange some dependencies now that we're dropping py34 from the build
matrix (pytest-cov has some issues on Travis with py34)

* try rolling back pytest-cov

* add filechunkio dependency; move pytest-cov back to pip requirements (version update to follow)

* move newer pytest-cov to conda requirements

* disable errexit on tests-long.sh

* pytestcov testing

* bump pytest-cov version, add sleep 2

* add pysftp to py3 requirements

* change config.yaml paths to s3

* restore env_vars in snakemake config

* decrease memory for picard in align_rna test

* let's try omitting pytest-xdist

* "py.test" -> "pytest"

* roll back explicit coverage dependency, rollback pytest-cov

* pytest --exitfirst to exit on first failure

* extend sleep in tests to hopefully allow logs to be fully printed on Travis

* Travis:  sudo: true;  dist: trusty

experimenting with travis to speed up builds; seeing if sudo:true helps
at all…

* py3 requirements conda and pip friendly

* unset errexit in travis tests

* exit with error

* sleep and exit with error, on error

* roll back boto

* touch ~/.boto

* decrease thread count in taxon filter integration tests

* remote ~/.boto experiment

* boto to 2.48.0 again, and add conda clean step

* sta... (continued)

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