run_dbcan - 4.1.4

Update to 4.1.4

1. Fix bugs in cgcfinder
2. Add --verbose
3. Fix syntenic_plot bug
4. Fix other bugs

run_dbcan-4.1.3

• Add dependency blast, requests
• Fix bugs in the installation part of the document.
• Fix bugs in dbcan_build

run_dbcan-4.1.1

• Fix bug in dbcan_plot
• Add dbcan_build function so user can directly use dbcan_build to install the database and build an index.

run_dbcan-4.1.2

1. Fix bug for gff file judgement
2. Add dependencies matplotlib, openpyxl
3. Fix other bugs

run_dbcan-4.1.0

Release run-dbCAN-4.1.0

Comprehensive reconstruction of the run-dbCAN framework has been completed. Multiple functions have been annotated for enhanced clarity. Documentation is currently being written and will be available on ReadTheDocs [Haidong].

Integration of dbCAN protocol for both downstream and upstream analysis has been added. For detailed information, please refer to the user guide at https://dbcan.readthedocs.io/en/latest/user_guide/run_from_raw_reads.html [Jinfang].

The process of creating ReadTheDocs documentation for dbCAN is underway https://dbcan.readthedocs.io/en/latest/index.html. This includes harmonizing dbCAN with both downstream and upstream analysis. Additionally, several bugs identified through user comments and issues have been addressed and resolved [Le].

run_dbcan-4.0.0

-Replace ECAMI with dbCAN_sub.
-Fix some bugs

dbCAN-3.0.7

• Fix hmmscan_parser.py bug

dbCAN-3.0.6

Here is the new release for dbCAN-3.0.6.
-1. Replace Hotpep with eCAMI
-2. Fix sum bugs
-3. Publish Bioconda version

Release run_dbcan 3.0

Update Info

• V3.0.2 please use pip install dbcan==3.0.2 for update
  • Added eCAMI tool, remove Hotpep from run_dbCAN;
  • Changed the format of cgc.out to make it easy to read;
  • Fixed ‘-t all’ will cause the program to generate empty files.
  • Updated CAZy db for Diamond and HMMER DB for HMMER.
  • Re-arranged the code. The command line is run_dbcan without the suffix .py. Please check the command lines below.
  • The database files under db folder is now hosted through Git-LFS. To download the complete db files, please use the command git lfs pull (Note: To use git lfs, please check the installation guide at https://git-lfs.github.com/).
  • Docker file is updated and we simplify the installation step.
  • Fix the bug of the file path.