Download and use SRAs; add SingleCellProteogenomics to pipeline

Update pipeline to download and use SRAs from GEO (#1)

* rework from sra-download

* linting

* through sras and trimming

* through making rsem-star reference

* adding velocity calculations

* working through making a_obs

* copying new results

* finish pipeline through making dataframes

* comment out testing

* update input link

* add kinase results to all to prompt full run