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dbman - (biological) Database Manager
=====================================
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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. 
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Supported Databases with associated tools:

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

Installation
------------

Prerequisites:

* Python (Version >= 3.7)
* Git

Install for user::

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    pip install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbman.git
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Install for developers::
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    #checkout repository
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    git clone git@git.computational.bio.uni-giessen.de/SOaAS/dbman.git
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    #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
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    dbman prepare example/database example/tool
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Transfer databases from the working computer to s3 Cloud::

    # check the available optional parameters
    dbman upload -h

    # run the standard transfer
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    dbman upload example/database example/tool*
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Transfer databases from s3 Cloud to working computer::

    # check the available optional parameters
    dbman download -h

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

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Configure database storage directories via environment variables:: 
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    # set local database directory, default "./"
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    export DBMAN_DBDIR = example/path

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    # 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
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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'.