Running PR for Snakemakeification #164
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[MRG] change busco wrapper to enable config
Unify click and argparse interfaces
Migrate config and temp file locations, conform output filenames to v1.2 format
Plot busco
Tests each dammit CLI component and each dammit snakemake wrapper. Updates pytest infrastructure by adding fixtures for snakemake invocation and new environment variables.
* use snakemake 5.20.1; install mamba in environment.yml * use mamba for conda installations
* Fix some module imports in dammit tests * Remove deprecated / unused functions * remove unused busco_config * Update some project configs * add envs to gitignore * fix BUSCO for multiple lineages, proper output tracking, summary plot generation * Final directory restructure of BUSCO for multiple lineages * Fix major bug with -o output dir * Remove unused JSON config files * Add printed banner during dammit run exection * add pom 20 * Remove busco default config ini as rule input; otherwise, the file is changed on reinstall and the rule is rerun * Fix checkpoint directory removal in transdecoder wrappers * Remove dammit.fileio and use ope.io instead * Fix parameter name in remap command function * Add hmmer remap step * remove setuptools bootstrap * remove bootstrap * update generate-test-data for new CLI * fix BUSCO config problem yet again and bump version to 4.1.4 * update first integration test with bigger file and proper test data * Opeify (#198) * Add ope req to setup * hmmscan wrapper uses ope when n_threads is greater than 1 * Add 5 transcript pom subset * opeify lastal wrapper * opeify infernal wrapper * Fix README format in setup.py and MANIFEST * register --global-evalue with config * Fix thresholding, TransDecoder params * remove unused test data * update pom.20 test data results * collapse test_threaded into test_annotate_default * add regenerated pom.20 test data * add --max-threads-per-task command line switch * Further reorgnization of integration tests; update --global-evalue test for new CLI API * Update generate-test-data for new CLI API * some clean-up
#200) * Move GFF3 conversion code back into dammit and use new ope GFF3Convert abstract base class * set show_default=True on most command line options * Constrain MANIFEST globbing of wrappers * improve test output * remove unused import: * bump to ope 0.8 in all environments * Update test data for fixed ope GFF3 ID generation * set ignore_errors=True on config deletion * bump ope version in shmlast wrapper environment * formatting * Split apart internal and user config files; rearrange global access * fix BUSCO test rule, change db_dir var name * Fix incorrect config access in cmscan step * Fix n_threads and max_threads_per_task defaults and interplay * Use absolute paths for directories; fail on annotate when databases are not installed * make banner ~~~gay~~~ * Update evalue test data
…tic location of conda environment during test sessions; tempdir_factory is used per-session if this variable is not defined
Add an environment variable DAMMIT_TESTING_TEMP_BASE_DIR to set a sta…
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See https://github.com/dib-lab/dammit/projects/1.