2. Quick start

[npavlovikj@login.crane ~]$ git clone https://github.com/npavlovikj/ProkEvo.git
[npavlovikj@login.crane ~]$ cd ProkEvo/

To download raw Illumina paired-end reads from NCBI, as an input, ProkEvo requires only a list of SRA ids stored in the file sra_ids.txt. In this repo, as an example we provide file sra_ids.txt with few Salmonella enterica subsp. enterica serovar Enteritidis genomes:

[npavlovikj@login.crane ProkEvo]$ cat sra_ids.txt 
SRR5160663
SRR8385633
SRR9984383

Once the input files are specified, the next step is to submit ProkEvo using the provided submit.sh script:

[npavlovikj@login.crane ProkEvo]$ ./submit.sh 

And that's it! The submit script sets the current directory as a working directory where all temporary and final outputs are stored. Running ./submit.sh prints lots of useful information on the command line, including how to check the status of the workflow and remove it if necessary.