This menu is used for running external programs on UNIX and is not available on other operating systems. Once configured correctly, running an external program should be as simple as selecting some features of interest, then choosing one of the items from the run menu. When the external programs finishes the results can viewed using the "Search Results" item in the View menu (see the section called Search Results).
To use this feature the run_blastp, run_fasta etc. scripts that are supplied with Artemis will need to be changed to reflect the paths and databases that are configured at each site.
Each external program that is listed in the options file (see the section called feature_dna_programs in Chapter 4 and the section called feature_protein_programs in Chapter 4) gets a "run" menu item and a "set options" menu item. For each external program (such as blastp) there must be a shell script available that sets any necessary environment variables and then launches the search/analysis program (for blastp the script is called run_blastp).
Taking blastp as an example, this is the sequence of events that occurs when the user selects the "Run blastp on selected features" menu item:
Artemis creates a new directory in the current directory called blastp.
A protein FASTA sequence file is written in the new directory for each selected feature. (For a DNA search program such as blastn the file will be a DNA FASTA file). The sequence file name will be something like: /blastp_file="blastp/features.tab.seq.00001".
The name of the expected output file is stored in the feature in a qualifier called /blastp_file. If the entry is called features.tab then the qualifier will be set to something like: /blastp_file="blastp/features.tab.seq.00001.out". Note that because the file name is stored in the entry you will need to save the entry to keep the association between the features and the output files.
A file is then written (called file_of_filenames.blastp) that contains the names of all the newly created sequence files in the blastp directory.
Artemis then tries to read the run_blastp script from the Artemis installation directory. The script is executed like this:
run_blastp file_of_filenames.blastp [options]
where [options] currently must be a single word (normally a database to search). In the case of blastp/blastn/fasta etc. the second argument of the script is passed directly to the blast/fasta as the database name. For testing purposes it is possible to run run_blastp on the command line with the same arguments as above.
run_blastp will run blastp on each of the sequence files listed in file_of_filenames.blastp and save the output in the corresponding .out file.
If the program is successfully started, control will immediately return to the user. When run_blastp finishes a message will be displayed to alert the user.
If necessary, it is possible to exit once Artemis indicates that the external program has been started and the entry has been saved. run_blastp will keep running in the background.