DRAM 1.5.0 release

This is the official release of DRAM1.5.0. The 1.5.0 release has significant changes that could impact your research. Please review these changes and help us validate this release!

Install / upgrade:

If DRAM is installed with Bioconda, and then it can be upgraded like any Conda package. Note that the Conda package for dram may be delayed slightly while it is validated, but it should be available within a day or two of the release.

If you already have a DRAM environment and want to upgrade:

# Activate your old DRAM environment first!
# Save your old config
DRAM-setup.py export_config > my_old_config.txt
# install DRAM
wget https://raw.githubusercontent.com/shafferm/DRAM/master/environment.yaml
conda env update -f environment.yaml -n DRAM --prune
# import your old databases
DRAM-setup.py import_config --config_loc  my_old_config.txt

If you are using an old database, like in the example above, you may need to check out a special version of dram from GitHub.

git clone https://github.com/WrightonLabCSU/DRAM.git
cd DRAM
git checkout dbcan_no_ec
conda env update -f environment.yaml -n DRAM --prune
conda activate DRAM
conda install pip
pip install ./

To install the DRAM in a new Conda environment, follow the instructions in the README.

Change log DRAM1.5.0:

1. DRAM annotate now has a new database which may be included. The new database CAMPER (Curated Annotations for Microbial (Poly)phenol Enzymes and Reactions) can be incorporated into DRAM.

Please visit the CAMPER GitHub for more information: https://github.com/WrightonLabCSU/CAMPER

2. Accumulation of mmseq temporary files during annotation are now removed immediately after a given sample has processed. Before, these files were removed after all samples were annotated. This reduces storage space needed for a given DRAM run.

3. "scikit-bio" related error. This error arose when scikit-bio was updated. While always using the latest version of a software can be important for security updates, the stability of DRAM is our main concern. To solve this, we have explicitly stated each version of each dependency within the environment.yaml file.