You're right, I didn't make it clear! I downloaded qualscore from: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/qualscore/
I did have the supporting files in a /lib subdirectory under TPP/bin, but upon closer inspection it looks like one had a corrupted download. Upon re-downloading I could see the help message when running qualscore without arguments at the command line. However when running it via Petunia, I now get the following output: > EXECUTING: cd e:/proj&& java -jar C:/TPP/bin/qualscore.jar -c 1.0 -p 0.1 > interact.pep.xml > QualScore version 1.0_2 Copyright (C) 2006 > Institute for Systems Biology, Seattle WA > QualScore is free software and comes with absolutely no warranty. > ERROR: Cannot find interact.pep.xml If I copy the above command and paste it in the console I get a different error stating that the mzXML could not be found. This is likely because I'm using mzML which may be unsupported by QualScore. I'll try to reconvert to mzXML and run from the command line. On Wed, Jan 4, 2017 at 11:56 AM, Eric Deutsch <[email protected]> wrote: > Maybe you’ve done this, but from your description it’s not clear, I think > the lib jars must be in a lib/ subdirectory, not in the same directory as > the main qualscore.jar. > > > > Eric > > > > > > *From:* [email protected] [mailto:spctools-discuss@ > googlegroups.com] *On Behalf Of *Jason Winget > *Sent:* Tuesday, January 03, 2017 7:59 AM > *To:* spctools-discuss > *Subject:* [spctools-discuss] Is QualScore still shipped with/supported > by the TPP? > > > > I'm trying to run QualScore via the "Rescue Peptides" menu item under TPP > Tools in Petunia. > > Initially this returned an error that qualscore.jar couldn't be found, and > indeed it was not in TPP/bin. I downloaded the most recent qualscore jar > from sourceforge and placed it as well as the /lib/ jar files into TPP/bin, > and now get the following errors: > > > > java.lang.NoClassDefFoundError: org/jfree/data/SeriesDataset > > at java.lang.Class.getDeclaredMethods0(Native Method) > > at java.lang.Class.privateGetDeclaredMethods(Unknown Source) > > at java.lang.Class.privateGetMethodRecursive(Unknown Source) > > at java.lang.Class.getMethod0(Unknown Source) > > at java.lang.Class.getMethod(Unknown Source) > > at sun.launcher.LauncherHelper.validateMainClass(Unknown Source) > > at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source) > > Caused by: java.lang.ClassNotFoundException: org.jfree.data.SeriesDataset > > at java.net.URLClassLoader.findClass(Unknown Source) > > at java.lang.ClassLoader.loadClass(Unknown Source) > > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) > > at java.lang.ClassLoader.loadClass(Unknown Source) > > ... 7 more > > Error: A JNI error has occurred, please check your installation and try > again > > Exception in thread "main" > > > > TPP version information: > TPP v5.0.0 Typhoon, Build 201610111222-7423 (Windows_NT-x86_64) > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/3_prIdWwEd4/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
