re-adding bioconda install instructions #7
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demo notebook update, config update, tests update
* moving docs from wiki to git * fix more image references * fix more links * added pip install instructions * change command line to use the insilicosv CLI entry point. remove docs about deleted scripts generate_synthetic_genome.sh and divergent_repeat_augmentation.sh
Added conda environment for running the demo notebook
…nstructions docs: README.md install instructions changed to use pip or bioconda
README updates (directory setup for user)
…pped transformed ref to original ref
* demo notebook update, config update, tests update * PR updates to demo notebook * move wiki to git (#1) * moving docs from wiki to git * fix more image references * fix more links * added pip install instructions * change command line to use the insilicosv CLI entry point. remove docs about deleted scripts generate_synthetic_genome.sh and divergent_repeat_augmentation.sh * removing install/ dir for now, obsoleted by pip install (#2) * .gitignore: added notebook outputs * update version to 0.0.5 * move license to pyproject.toml * demo notebook fixes * adding demo notebook conda env definition * change pbsim3 model path * insilicosv-demo-env: added minimap2 * use pbsim3 model from the pbsim3 conda package * added igv to demo notebook conda env * made simulated read coverage configurable in demo notebook via env vars * update demo notebook env to current igv * fix env name * .gitignore: add IGV_screenshots * adding the original definition of insilicosv-demo-env * .gitignore: added workflow-related ignores * docs: README.md install instructions changed to use pip or bioconda * change references to simulate.py into references to insilicosv executable script * added demo notebook instructions * docs: README.md -- clarified where to find config file syntax * fixed image link for the grammar * added space around image ref * added more spaces around image refs to ensure correct display on github * removed divergent repeat example visualization * README updates (directory setup for user) * removed, for now, documentation reference to the utility code that mapped transformed ref to original ref * removed get_original_base_pos() from utils.py for now * removed div_repeat_postproc * doc: remove stray line * docs: remove duplicate line * docs: drop mention of wiki * docs: removed mentions of not-yet-released functionality --------- Co-authored-by: crohlicek <[email protected]> Co-authored-by: Chris Rohlicek <[email protected]>
* updates to docs * info about rel/abs path for reference in config * INDEL support mentioned, default sim settings removed from example configs * added small config example to input_guidelines page * mention of SVs replaced with variants in places where SNPs are meant to be included * example config in input_guidelines changed to use lists for input sizes * remove statement of rel/abs ref path; include mention of output insertions.fa file * clarifying terminology * moving summary config github gist to dedicated .md file in docs/ * link to example_use_cases.md given with more explanation * adding mention of ref as config input * included descriptions of all config inputs with links to examples in input format description
* removed usage of order in output bed format, and changed nth_sv to sv_id * removed unused code * adding back internal logic for order
* config now accepts min_lengths and max_lengths inputs of type list only * updated demo config to use lists for input sizes * example_use_cases.md updated with configs that use lists for input sizes * avoid_intervals moved to top level of confi * SVs config field replaces with variant_sets; related changes to docs and tests * clarified config file format * fix to old default stored for filter_small_chr * removal of forced HOM for div_dDUPs (a requirement for div. repeats) --------- Co-authored-by: Ilya Shlyakhter <[email protected]>
* updates / typo corrections to demo notebook markdown cells * change description of PBSIM read combination step
…nv.yml, since our docs say to use the platform-agnostic insilicosv-demo-env.reqs.txt
…version of insilicosv but bioconda does not yet
crohlicek
approved these changes
Dec 13, 2023
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