paths.txt is always written where .jar is located no matter temp settings

[CarlosHorro]

When running PS in Galaxy it uses "-temp_folder" option, but still paths.txt is always written into the same folder than the .jar is located:

java.lang.RuntimeException: java.io.FileNotFoundException: /usr/local/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt (Permission denied)
at com.compomics.util.io.flat.SimpleFileWriter.(SimpleFileWriter.java:59)
at eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.writeConfigurationToFile(PeptideShakerPathParameters.java:391)
at eu.isas.peptideshaker.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:110)
at eu.isas.peptideshaker.cmd.PathSettingsCLI.extractAndUpdatePathOptions(PathSettingsCLI.java:269)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1366)
Caused by: java.io.FileNotFoundException: /usr/local/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt (Permission denied)
at java.base/java.io.FileOutputStream.open0(Native Method)
at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298)
at java.base/java.io.FileOutputStream.(FileOutputStream.java:237)
at java.base/java.io.FileOutputStream.(FileOutputStream.java:187)
at java.base/java.io.FileWriter.(FileWriter.java:96)
at com.compomics.util.io.flat.SimpleFileWriter.(SimpleFileWriter.java:53)
... 4 more

UtilitiesPathParameters.configurationFileName have to be properly managed in PathSettingsCLI.

[bernt-matthias]

This still happens in the latest version .. (2.0.25)

[hbarsnes]

This still happens in the latest version .. (2.0.25)

I know. It has not been looked into yet. Hence the reason why the issue is still open. ;)