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 'example/tool' enter 'raw'.   

blast_swissprot.sh

-#!/bin/bash
-
-DOWNLOAD_DIR=$1
-
-cd $DOWNLOAD_DIR
-makeblastdb -dbtype prot -in ../dbx/uniprot_sprot.fasta
-tar -czf sp_blast.tar.gz uniprot_sprot.*
-rm uniprot_sprot*
-cd -
\ No newline at end of file

dbman.egg-info/PKG-INFO

+Metadata-Version: 1.0
+Name: dbman
+Version: 0.0.1.dev14
+Summary: Download, convert and upload databases to cloud server
+Home-page: UNKNOWN
+Author: Rudel Fankep
+Author-email: Rudel.C.NKouamedjo-fankep@bio.uni-giessen.de
+License: MIT
+Project-URL: Source Code, https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git
+Description: Download, convert and upload databases to cloud server
+Keywords: tools, databases
+Platform: UNKNOWN

dbman.egg-info/SOURCES.txt

+README.rst
+requirements.txt
+setup.cfg
+setup.py
+test.py
+testfile.txt
+dbman/__init__.py
+dbman/main.py
+dbman.egg-info/PKG-INFO
+dbman.egg-info/SOURCES.txt
+dbman.egg-info/dependency_links.txt
+dbman.egg-info/entry_points.txt
+dbman.egg-info/not-zip-safe
+dbman.egg-info/pbr.json
+dbman.egg-info/requires.txt
+dbman.egg-info/top_level.txt
+dbman/scripts/blast_db.sh
+dbman/scripts/delete_remote_file.sh
+dbman/scripts/download_db.sh
+dbman/scripts/download_json.sh
+dbman/scripts/ghostx_db.sh
+dbman/scripts/hmmer_pfam.sh
+dbman/scripts/prepare_card.sh
+dbman/scripts/prepare_pfam.sh
+dbman/scripts/prepare_swissprot.sh
+dbman/scripts/upload_db.sh
+dbman/scripts/upload_json.sh
+local_databases/dbman_metadata.json
+local_databases/swissprot_2019_06_blast/uniprot_sprot.fasta.phr
+local_databases/swissprot_2019_06_blast/uniprot_sprot.fasta.pin
+local_databases/swissprot_2019_06_blast/uniprot_sprot.fasta.psq
\ No newline at end of file

dbman.egg-info/dependency_links.txt

+

dbman.egg-info/entry_points.txt

+[console_scripts]
+dbman = dbman.main:main
+

dbman.egg-info/not-zip-safe

+

dbman.egg-info/pbr.json

+{"git_version": "2b012ee", "is_release": false}
\ No newline at end of file

dbman.egg-info/requires.txt

+wget

dbman.egg-info/top_level.txt

+dbman

dbman/scripts/blast_db.sh

+#!/bin/bash
+
+TOOL_DIRECTORY=$1
+TOOL_FILE=$2
+
+
+cd $TOOL_DIRECTORY
+makeblastdb -dbtype prot -in $TOOL_FILE
+cd -
\ No newline at end of file

dbman/scripts/delete_remote_file.sh

+#!/bin/bash
+
+REMOTE_FILE=$1
+s3cmd del $REMOTE_FILE 
\ No newline at end of file

dbman/scripts/download_db.sh

+#!/bin/bash
+REMOTE_TARFILE=$1
+LOCAL_DATABASE_DIRECTORY=$2
+TARFILE=$3
+cd $LOCAL_DATABASE_DIRECTORY
+s3cmd get $REMOTE_TARFILE 
+tar -xzvf $TARFILE
+rm $TARFILE
+cd -
\ No newline at end of file

dbman/scripts/download_json.sh

+#!/bin/bash
+REMOTE_FILE=$1
+LOCAL_DATABASE_DIRECTORY=$2
+
+cd $LOCAL_DATABASE_DIRECTORY
+s3cmd get $REMOTE_FILE 
+cd -
\ No newline at end of file

dbman/scripts/ghostx_db.sh

+#!/bin/bash
+
+TOOL_DIRECTORY=$1
+RAW_FILE=$2
+cd $TOOL_DIRECTORY
+ghostx db -i $RAW_FILE -o ghostx_db
+cd -
\ No newline at end of file

dbman/scripts/hmmer_pfam.sh

+#!/bin/bash
+TOOL_DIRECTORY=$1
+RAW_FILE=$2
+
+
+cd $TOOL_DIRECTORY
+hmmpress $RAW_FILE
+cd -
\ No newline at end of file