Updating Databases

Updating the database is supper simple and foremost you will just run:

dram2 -d <where to put the db> build_db

To put the config in a specific location:

dram2 -d <where to put the db> build_db -y <yaml_loc>

To update:

dram2 -d <where to put the db> build_db  -u

To make only a few dbs:

dram2 -d <where to put the db> build_db  --make_db <db_name>

What about kegg and camper

KEGG will always need to be independently downloaded and CAMPER to while its repository is private. The input argument lets you do this.

Download

For CAMPER just go to the release page on the github page and download the tag_gz release.

For KEGG use the scripts in this repository, here: https://github.com/WrightonLabCSU/DRAM2/tree/main/extra/kegg_tools You need to clone the repository or download the zip and copy all the scripts to a folder on a disk with lots of space. Then you will run them. You can’t just get the script because we have the repo as private.

This is easy, all you need is a username and password. You must run the next command in screen or tmux, and you will be prompted for your passwords. This will run a long time and download a bunch of stuff:

./download_kegg.sh

Now you will have a folder full of files. Don’t change directories, don’t change the folder. Run format_kegg.py on the screen or as a big slurm job in the same directory. You will probably need to activate a dram conda environment, any version of dram, to get the paths you need. The command is:

python format_kegg.py

Now you have one pep file “kegg-all-orgs_unique_reheader.pep” ready for DRAM.

Pass File locations

To see the arguments and keys for the setting file locations, you can use:

dram2 build_db_list

The command to update camper and KEGG is then:

dram2 -d <output for db> build_db -u --make_db camper --make_db kegg -i <kegg_pep>
-i camper_tar_gz <path to the tar file>

Do read the help for more info.