add Wastyk2021 dataset to doc #150
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linnabrown
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Jan 18, 2024
* dbcan 3.x development (#141) * move cli to the pkg * add .editorconfig * add pre-commit-config.yaml * add .dockerignore * reformat * rm setup script and conf * change ValueError to KeyError * add readthedocs conf * add .toml to manage the proj * add sphinx docs * .dockerignore * add user guide doc * simplify readme * reorder authors * :Update 4.1.0: 1. Update dbCAN 2. Harmonizing codes from Jinfang's updates * fix small bugs * update dbCAN version * revise sha256 for 4.1.0 * add yml file to install environment for dbcan-protocol * remove usage * :add: readthedoc badge * [fix] fix bug in meta.yaml * [Update docs/user_guide/database_preparation.rst] Installation method * [Update] rename sub.prediction.out into substrate.out * 1. rename dbcan_cli into dbcan.cli in plots.py 2. add seaborn in dbcan.yml 3. update run from raw reads rst file 4. fix pyproject.toml for typo * move Dockerfile to root * add cazyme annotation Dockerfile * remove git-lfs db * [Fix] reformat readTheDoc docs/user_guide/run_from_raw_reads.rst * [Fix] docs/user_guide/run_from_raw_reads.rst :fix some grammar issue for rst format: * 1. [update] dbcan/cli/run_dbcan.py 2. [add] add dbcan/cli/dbcan_build.py for database build, add entrypoint in pyproject and meta.yaml * delete redundant file * [fix] remove number after reference * add refs for datasets * add Wastyk2021 dataset to doc (#150) * fix typo * add dbcan_build * revise meta.yaml * fix bug in installation * add database * [fix] fix command error in installation.rst * revise the doc * revise * 1. fix bug in dbcan_sub; 2. add packages matplotlib, openpyxl * update dbcan_build * fix but for gff judgement * revise dependencies * fix bug in the docs * revise run from protein sequence to run from DNA sequence * remove the database installation page. remove pip install part * update docker * 1. add requests package 2. fix bug in dbcan_build * Fix issues in readthedoc * polish the catalog page --------- Co-authored-by: HD Yi <haidyi@cs.unc.edu>
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This pr includes the following patches:
Wastyk2021dataset