Note: before you begin the exercise, make sure you add /apps/unit/MikheyevU/sasha/miniconda3/bin to your PATH.
The objective is to create a tab-delimited database of countries, capitals and currencies, like that in data/countries, capitals and currencies.txt. To do this, you have two pairs of files, one pair containig countries and currencies, and another pair containing countries and capitals.
I suggest getting the script working on the head node first, without using sbatch, and doing the job submission as part of the last step.
- Clone the repository
- Make a branch with your own name, and switch to that branch
- Write a snakemake rule that processes each pair of country/capital and country/currency files, creating a pair of tab-delimited country/capital/currency files. This rule should act on each pair separately, i.e., using two separate tasks that can, in principle, be run in parallel.
- Write a rule that combines the output of the previous rule into a single file, containing a tab-delimited database with all the data.
- Write a rule verifying that the information content in your output corresponds to that of the reference database in
data/countries, capitals and currencies.txt - Run the jobs on sango, add sango logs to the repository, commit them to the repo and push the results to github.