added gem files and initial code to download and run data
bin directory and executable
fix installing dependencies and downloading data
Changed data description from json to yaml
Now stores hierarchy of files
Added filenames of assemblies to data description
Parse urls, download only if necessary and extract files
added option to fastq-dump to restore original deflines to fastq file
added human and yeast experiments from corset dataset; removed chicken
construct transrate commands from data
create directories
check whether to use curl or wget
creating directories again
check if directories already exist
fixed syntax errors
run the transrate command for each experiment/assembler
add transrate as a dependency...duh
separate transrate run for each reference
made file paths absolute
fixed read file paths
added another yeast reference; check if transrate has already been run
switched temp dropbox link back to zenodo