I have not been able to use custom exports when using Reporter from (linux) command line.
It works successfully in Windows GUI (creating exportFactory.json and exporting the report) and then I will use the same exportFactory.json from the command line.
paths.txt contains the proper directory:
reporter_exports=/home/jamie/jcms_projects/jc/pnnl/scripts/reporter
Within this directory is exportFactory.json generated as mentioned above.
Running reporter then generates the log entry showing the custom report isn't recognized:
java.lang.IllegalArgumentException: Unrecognized report type: 13. Available reports are: 0: Certificate of Analysis, 1: Default Hierarchical Report, 2: Default PSM Phosphorylation Report, 3: Default PSM Report, 4: Default PSM Report with non-validated matches, 5: Default Peptide Phosphorylation Report, 6: Default Peptide Report, 7: Default Peptide Report with non-validated matches, 8: Default Protein Phosphorylation Report, 9: Default Protein Report, 10: Default Protein Report with non-validated matches, 11: Extended PSM Report, 12: Fractions Report.
at eu.isas.peptideshaker.export.PSExportFactory.getExportTypeFromCommandLineOption(PSExportFactory.java:749)
at eu.isas.reporter.cli.ReportCLIInputBean.<init>(ReportCLIInputBean.java:68)
at eu.isas.reporter.cli.ReporterCLIInputBean.<init>(ReporterCLIInputBean.java:335)
at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:352)
at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)
I noticed paths.txt also has a peptideshaker_exports entry so I manually updated it to be the directory above.
peptideshaker_exports=/home/jamie/jcms_projects/jc/pnnl/scripts/reporter
Now if I run reporter, I get the following log entry:
java.io.FileNotFoundException: File resources not found.
at eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.loadPathParametersFromLine(PeptideShakerPathParameters.java:214)
at eu.isas.reporter.preferences.ReporterPathPreferences.loadPathParametersFromLine(ReporterPathPreferences.java:153)
at eu.isas.reporter.preferences.ReporterPathPreferences.loadPathParametersFromFile(ReporterPathPreferences.java:126)
at eu.isas.reporter.cli.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:132)
at eu.isas.reporter.cli.PathSettingsCLI.extractAndUpdatePathOptions(PathSettingsCLI.java:275)
at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:822)
Furthermore, now within the exports directory listed above is the file: reporter_exportFactory.cus containing:
The next thing I tried is renaming exportFactory.json that I generated to both reporter_exportFactory.json and reporter_exportFactory.cus but neither helped (same log entries mentioned above).
Anyway, I haven't been able to find any sort of workaround to get this issue resolved to be able to suggest how it can be fixed.
I'll also note that I have no problems using exportFactory.json (generated in Windows PeptideShaker) in the command-line version of PeptideShaker.
Thanks!