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dbman - (biological) Database Manager

This tool is a collection of scripts with a lean frontend to download, prepare and distribute (biological sequence) databases.

Homology analyses with different tools require the reference databases to be available locally and to be compiled for the respective tool. In distributed environments, e.g. the cloud these compiled databases have to be made available on all required computers. This tool helps with these steps: download, prepare/compile for different tools and distribution via upload/download to/from S3.

Supported Databases with associated tools:

  • Uniprot-Swissprot [Blast, Ghostx]
  • CARD [Blast, Ghostx]
  • Pfam [hmmer]

Installation

Prerequisites:

  • Python (Version >= 3.7)
  • Git

Install for user:

pip install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbman.git

Install for developers:

#checkout repository
git clone git@git.computational.bio.uni-giessen.de/SOaAS/dbman.git

#install
pip3 install -e .

Using Database Manager

For the general help use:

dbman --help

Checkout which databases are available:

# in the S3 directory
dbman list_remote_databases

# in the local directory
dbman list_local_databases

Checkout which databases with associated transformations are available:

dbman list_recipes

Prepare databases:

# check the available optional parameters
dbman prepare -h

# run the standard preparation
dbman prepare example/database example/tool

Transfer databases from the working computer to s3 Cloud:

# check the available optional parameters
dbman upload -h

# run the standard transfer
dbman upload example/database example/tool*

Transfer databases from s3 Cloud to working computer:

# check the available optional parameters
dbman download -h

# run the standard download
dbman download example/database example/tool*

Delete undesirable databases:

# from the local directory
dbman delete example/database example/tool* local

# from the s3 cloud directory
dbman delete example/database example/tool* s3

Configure database storage directories via environment variables:

# set local database directory, default "./"
export DBMAN_DBDIR = example/path

# s3 support is based on s3cmd. See its manual to setup s3
# set subdirectory in s3 bucket, default is s3://db_storage
export DBMAN_S3DIR = s3://example/path

The standard directories(local and remote) can also be change with optional parameters.

(*) For upload, download and delete of the raw databank instead of 'example/tool' enter 'raw'.