Do all script

[davidonlaptop]

Write a script that runs all the other scripts so that the 1000 Genome Project can be synchronized with one single command.

Particular behavior

• The script should output the date (HH:mm:ss) at each step and log to stdout its progress

Execution Example

Example of how this script could be called:

./sync1kg.sh

Contents Example

If all other files adhere to the specified examples, this file should have a content similar to:

#!/bin/bash

echo "Creating directory for holding temporary files"
mkdir -p etl/

./src/files-crawler.sh ftp://ftp.ncbi.nlm.nih.gov/   >  etl/files.csv
./src/sequences-metadata.sh ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/sequence.index   >  etl/sequences.csv
./src/alignment-metadata.sh ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/alignment.index   >  etl/alignments.csv
./src/sample-metadata.sh ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.txt   >  etl/samples.csv
TODO: download population and superpopulations csv files

./src/load-mysql.sh etl/samples.csv etl/populations.csv etl/superpopulations.csv etl/sequences.csv etl/alignments.csv etl/files.csv