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Section 2 Download Install Files
If you've constructed your config correctly then the following command should successfully download the genomes for yeast and the worm along with the homology data. But before you execute make sure that the staging and install locations in that config file are within the workshop directory.
cd ~/workshop
elt download -c <path to your config file>This took ~3 minutes on a mediocre internet connection.
If you look inside your staging directory, you will note there is a downloaded.cfg file. This is expanded to include all the species (which matters when only an alignment has been indicated) and has modified the install path to be relative to the staging directory.
elt install -d <path to your staging directory>This took ~30 seconds on my laptop using a single CPU.
If you take a look in the files that are included in the homology directory you will note that they include relationship information to species that you did not specify in the download. When we do the installation of homology data only the species included in the config file are retained in the homology data. This is also true for whole genome alignments. Only the species that were specified in the config file have alignment data recorded in the installation.
elt installed -i <path to install directory>This presents a summary of the data that has been installed. At present, it does not indicate that homology data has also been stored. This is a new feature that needs to be added. Any volunteers 😊?