Look for symlinked reference genomes

[jmtsuji]

Problem description

I ran BackBLAST release v2.0.0-alpha6 on a server running Ubuntu 20.04 LTS.

When a subject genome (in the subject_genome_directory) is a symlink, it is not added to the search pipeline.

Furthermore, if no detectable genome files are in the subject_genome_directory, BackBLAST exits with a very cryptic error message (realpath: missing operand).

Proposed solution

In generate_run_templates.sh, function add_subjects_to_config_file, the find command should include the -L flag to look for symlinks. In addition, a check should be added for whether any subject genome files were detected by find.

Possible complications

In general, generate_run_templates.sh should probably be moved to Python long-term.