Commit 4ee3d2b8 authored by Rudel Fankep's avatar Rudel Fankep
Browse files

Add readme

parent 37797c97
...@@ -7,6 +7,7 @@ so that other computer can be able to download the data from there. It's also po ...@@ -7,6 +7,7 @@ so that other computer can be able to download the data from there. It's also po
databases on the working computer and/or in the Cloud. databases on the working computer and/or in the Cloud.
Supported Databases with associated tools: Supported Databases with associated tools:
* Uniprot-Swissprot [Blast, Ghostx] * Uniprot-Swissprot [Blast, Ghostx]
* CARD [Blast, Ghostx] * CARD [Blast, Ghostx]
* Pfam [hmmer] * Pfam [hmmer]
...@@ -15,13 +16,16 @@ Installation ...@@ -15,13 +16,16 @@ Installation
------------ ------------
Prerequisites: Prerequisites:
* Python (Version >= 3.7) * Python (Version >= 3.7)
* Git * Git
Install for user:: Install for user::
pip install git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git pip install git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git
Install for developer:: Install for developer::
#checkout repository #checkout repository
git clone git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git git clone git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git
...@@ -31,10 +35,13 @@ Install for developer:: ...@@ -31,10 +35,13 @@ Install for developer::
Using Database Manager Using Database Manager
---------------------- ----------------------
For the general help use:: For the general help use::
dbman --help dbman --help
Checkout which databases are available:: Checkout which databases are available::
# in the S3 directory # in the S3 directory
dbman list_remote_databases dbman list_remote_databases
...@@ -42,35 +49,46 @@ Checkout which databases are available:: ...@@ -42,35 +49,46 @@ Checkout which databases are available::
dbman list_local_databases dbman list_local_databases
Checkout which databases with associated transformations are available:: Checkout which databases with associated transformations are available::
dbman list_recipes dbman list_recipes
Prepare databases:: Prepare databases::
# check the available optional parameters # check the available optional parameters
dbman prepare -h dbman prepare -h
# run the standard preparation # run the standard preparation
dbman prepare example/database exemple/tool dbman prepare example/database exemple/tool
Transfer databases from the working computer to s3 Cloud:: Transfer databases from the working computer to s3 Cloud::
# check the available optional parameters # check the available optional parameters
dbman upload -h dbman upload -h
# run the standard transfer # run the standard transfer
dbman upload example/database exemple/tool\* dbman upload example/database exemple/tool\*
Transfer databases from s3 Cloud to working computer:: Transfer databases from s3 Cloud to working computer::
# check the available optional parameters # check the available optional parameters
dbman download -h dbman download -h
# run the standard download # run the standard download
dbman download example/database exemple/tool\* dbman download example/database exemple/tool\*
Delete undesirable databases:: Delete undesirable databases::
# from the local directory # from the local directory
dbman delete example/database example/tool\* local dbman delete example/database example/tool\* local
# from the s3 cloud directory # from the s3 cloud directory
dbman delete example/database example/tool\* s3 dbman delete example/database example/tool\* s3
remplace the standard directory to save the data:: remplace the standard directory to save the data::
# change local directory with the environment variable # change local directory with the environment variable
export DBMAN_DBDIR = example/path export DBMAN_DBDIR = example/path
# change remote directory with the environment variable # change remote directory with the environment variable
export DBMAN_S3DIR = example/path export DBMAN_S3DIR = example/path
......
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