Testing Samplot

Run tests

Testing samplot is (should be) simple. Assuming you have the repository cloned locally, cd to the test/data/ directory and run the commands.sh script (you may choose to remove the existing test directories first to ensure that output is newly generated). You must have the hg19 human reference genome in bgzipped format to successfully run these tests. That reference can be downloaded using the commands described in the Get data section below.

cd test/data/
rm -r test_imgs/
rm -r test_site/
bash commands.sh

This will re-create the directories where the example images are stored and re-plot those images, as well as re-generating the test site.

Get data

To acquire the reference or if you desire to re-download the entire test dataset from the Genome in a Bottle website, run the subset_alignments.sh script (in that same directory). This will take a subset of the alignments from many very large alignment files and will download the reference as a fasta file. Be aware that this may take quite a while.

If you only want the reference genome, edit the subset_alignments.sh file and comment out (with # at start of line) all commands except the "download hg19 reference for cram" block

bash subset_alignments.sh