3.x (#145)

* 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

---------

Co-authored-by: HD Yi <[email protected]>

dbcan.yml

@@ -0,0 +1,31 @@
+name: CAZyme_annotation
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - agBiome
+dependencies:
+  - python=3.9
+  - prokka
+  - megahit
+  - trim-galore
+  - blast
+  - bwa
+  - diamond
+  - hmmer
+  - samtools
+  - bedtools
+  - seqkit
+  - kraken2
+  - seqtk
+  - flye
+  - minimap2
+  - mmseqs2
+  - dbcan
+  - numpy
+  - pandas
+  - scipy
+  - matplotlib
+  - openpyxl
+  - biopython
+  - bbtools