Database Manager

This tool provide the preparation of Databases for several bioinformaticians tools. The preparated databases can be used on the working computer or can be saved on the cloud Server(Amazon Web Service S3) so that other computer can be able to download the data from there. It's also possible to delete some undesirable databases on the working computer and/or in the Cloud.

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/cfankep/psotdb.git

Install for developer:

#checkout repository
git clone git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.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 exemple/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 exemple/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 exemple/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

remplace the standard directory to save the data:

# change local directory with the environment variable
export DBMAN_DBDIR = example/path

# change remote directory with the environment variable
export DBMAN_S3DIR = 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'.