reference-data-manager 0.5

Bioinformatics Reference Data Manager is an application used to download, backup and update of reference data, required for various bioinformatics analysis

Copyright (c) 2018 Government of Canada

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Description: # Bioinformatics Reference Data Manager (BRDM)

## Description
BRDM is an application used to automatically update, backup and restore the reference data that required for bioinformatic analysis.

## Requirements

* miniconda

## Deployment Procedures

* Download rdm_env_setting.yaml from github
```
wget https://raw.githubusercontent.com/AAFC-BICoE/reference-data-manager/dev/rdm_env_setting.yaml
```
* Create the conda environment for the program
```
conda env create -n rdm_env --file rdm_env_setting.yaml
```
## Run the program

* Set up the config file
* The location of the sample configuration file config.yaml.sample
```
/path/to/conda/envs/lib/python3.6/site-package/brdm
```
* Default option to set up the config file: Copy the sample configuration to config.yaml and modify config.yaml
```
cd /path/to/conda/envs/lib/python3.6/site-package/brdm
cp config.yaml.sample config.yaml
nano config.yaml
```
* If the location or the name of your configuration file is different with that of default option, the path of your config file has to be provided by argument --config-file

* view the options of the program
```
source activate rdm_env
brdm -h
```
* Run the program
```
source activate rdm_env
brdm [option]
(an example: brdm --update-ncbi-blast)
```

## Some suggestions for executing the program

* All the NCBI database should be updated outside of business hours. Abuse of the Entrez or NCBI services can lead to temporary
loss of access.

* Construct the precise queries for NCBI subsets
1. The purpose of the NCBI subsets is to construct database for specific markers in a group of taxa;
it is suggested to provide information such as names of the markers, taxa and range of the sequence length in a query.
2. Confirm and refine your queries by testing them on NCBI website.
3. Due to the approach of constructing the subset database, sequences (e.g. wgs) that not exist in NCBI nt database cannot be included in subset database. The condition such as "and not wgs" is suggested to be added in your queries, in order to get the appropriate accession IDs and sequences.
1. The approach of constructing the subset database: Only accession IDs for each subsets are downloaded directly from NCBI; Sequences are retrieved from NCBI nt blast database;
2. Ncbi nt blast database consists of GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences.


Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License