1. Install and test new program with sample data to ensure it runs
successfully from any directory (see Note 18).
2. Determine the input requirements and the output format of
new program.
3. Add a new resource name (e.g., program_Z) in an appropriate
configuration file:
[Resources]
name=VALIDATE,WOLF,TMHMM,PROGRAM_Z,EVIDENCE
4. Add a new section to the same configuration file. The easiest
way to do this is to copy an existing resource and amend
accordingly (see Fig. 3). The texts highlighted in red are the
only parts expected to be changed.
5. Create a new directory in install_dir/vacceed/new_species/
pipeline using the same name as the new resource (but in
lowercase; e.g., program_z).
6. Create two directories called “output” and “scripts” in the
program_z directory.
7. Copy “template_resource_script” from install_dir/vacceed/
new_species/pipeline/common_programs to install_dir/vacceed/new_species/pipeline/program_z.
8. Rename “template_resource_script” to a user-named file (e.g.,
program_z_script) (see Note 19).
Fig. 3 Example of new resource added to species configuration file
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Stephen J. Goodswen et al.