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README.rst

+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 'tool' enter 'raw'.