Mass spectronomy-based proteomics

This is a project used to demonstrate the sysnthesis functionality provided by APE.

The use case aims to demonstrate the usefulness of the synthesis approach for solving a workflow discovery problem in bioinformatics. The scenario was demonstrated in [[1]].

No1 use case describes the 1st Use Case described in the paper, labeled as No. 1.

Note

In order to be able to execute the generated workflows on the machine, the tools have to be annotated accordingly, and the corresponding software should be available.

In order to use the APE library from the command line, simply run the APE-<version>-executable.jar file using command:

java -jar APE-<version>-executable.jar [path_to_ape_configuration_file]

No 1

As an example, if you would download the APE-2.3.0-executable.jar to the root of APE_UseCases repository on your local machine, you could run this demo by executing the following command:

cd ~/git/APE_UseCases
java -jar APE-2.3.0-executable.jar MassSpectometry/No1/config.json

The results of the synthesis would be stored under the directory specified in the configuration file (solutions_dir_path parameter). The results of the synthesis would be:

solutions_dir_path/solutions.txt - First X candidate solutions in textual format, where X is the number of solutions specified in the config file (``solutions`` parameter)
solutions_dir_path/Figures/        - Workflow figures corresponding to the first Y solutions, where Y is the number of solutions specified in the config file (``number_of_generated_graphs`` parameter, 0 if not specified))
solutions_dir_path/Executables/  - Executable shell scripts corresponding to the first Z solution, where Z is the number of solutions specified in the config file (``number_of_execution_scripts`` parameter, 0 if not specified))
solutions_dir_path/CWL/ - CWL files corresponding to the first Q solution, where Q is the number of solutions specified in the config file (``number_of_cwl_files`` parameter, 0 if not specified)