bernt-matthias
commented
3 years ago In the Galaxy wrapper for mpa portable we do the following:
jar_dir=`mpa-portable -get_jar_dir` &&
cp -R \$jar_dir/conf .Open CarlaCristinaUranga opened 4 years ago
bernt-matthias
commented
3 years ago In the Galaxy wrapper for mpa portable we do the following:
jar_dir=`mpa-portable -get_jar_dir` &&
cp -R \$jar_dir/conf .
Hi could you please let me know why I am getting this error? Thanks!
(mpa-portable) curangalt-osx:Biofilm_proteins curanga$ mpa-portable de.mpa.cli.CmdLineInterface -xtandem 0 -msgf 1 -spectrum_files CU_2C_01.mgf -database /Users/curanga/Desktop/Biofilm_proteins/HOMD.fasta -missed_cleav 1 -prec_tol 10ppm -frag_tol 0.02Da -fragment_method 2 -output_folder /Users/curanga/Desktop/Biofilm_proteins/Out Mon May 18 10:21:08 PDT 2020 Creating peptide index file... Mon May 18 10:21:08 PDT 2020 Peptide index creation finished... Mon May 18 10:21:08 PDT 2020 Indexing MS/MS spectra... java.io.FileNotFoundException: conf/algorithm-properties.txt (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at de.mpa.task.ResourceProperties.loadResourcesSettings(ResourceProperties.java:69)
at de.mpa.task.ResourceProperties.(ResourceProperties.java:38)
at de.mpa.task.ResourceProperties.getInstance(ResourceProperties.java:49)
at de.mpa.task.Task.(Task.java:67)
at de.mpa.task.instances.SpectraTask.(SpectraTask.java:25)
at de.mpa.cli.CmdLineInterface.call(CmdLineInterface.java:243)
at de.mpa.cli.CmdLineInterface.(CmdLineInterface.java:79)
at de.mpa.cli.CmdLineInterface.main(CmdLineInterface.java:335)
java.lang.NullPointerException
at de.mpa.client.ui.DelegateColor.getRGB(DelegateColor.java:30)
at java.awt.Color.equals(Color.java:699)
at java.awt.Component.firePropertyChange(Component.java:8433)
at java.awt.Component.setForeground(Component.java:1782)
at javax.swing.JComponent.setForeground(JComponent.java:2704)
at org.jdesktop.swingx.plaf.basic.BasicTitledPanelUI$1.updateUI(BasicTitledPanelUI.java:196)
at javax.swing.JLabel.(JLabel.java:164)
at javax.swing.JLabel.(JLabel.java:194)
at org.jdesktop.swingx.plaf.basic.BasicTitledPanelUI$1.(BasicTitledPanelUI.java:191)
at org.jdesktop.swingx.plaf.basic.BasicTitledPanelUI.createAndConfigureCaption(BasicTitledPanelUI.java:191)
at org.jdesktop.swingx.plaf.basic.BasicTitledPanelUI.installUI(BasicTitledPanelUI.java:134)
at javax.swing.JComponent.setUI(JComponent.java:666)
at javax.swing.JPanel.setUI(JPanel.java:153)
at org.jdesktop.swingx.JXTitledPanel.setUI(JXTitledPanel.java:153)
at org.jdesktop.swingx.JXTitledPanel.updateUI(JXTitledPanel.java:180)
at javax.swing.JPanel.(JPanel.java:86)
at javax.swing.JPanel.(JPanel.java:109)
at javax.swing.JPanel.(JPanel.java:117)
at org.jdesktop.swingx.JXPanel.(JXPanel.java:128)
at org.jdesktop.swingx.JXTitledPanel.(JXTitledPanel.java:127)
at de.mpa.client.ui.PanelConfig$2.(PanelConfig.java:117)
at de.mpa.client.ui.PanelConfig.createTitledPanel(PanelConfig.java:117)
at de.mpa.client.ui.PanelConfig.createTitledPanel(PanelConfig.java:104)
at de.mpa.client.ui.panels.ProjectPanel.initComponents(ProjectPanel.java:179)
at de.mpa.client.ui.panels.ProjectPanel.(ProjectPanel.java:144)
at de.mpa.client.ui.ClientFrame.initComponents(ClientFrame.java:246)
at de.mpa.client.ui.ClientFrame.(ClientFrame.java:165)
at de.mpa.client.ui.ClientFrame.getInstance(ClientFrame.java:136)
at de.mpa.client.ui.ClientFrame.getInstance(ClientFrame.java:126)
at de.mpa.task.ResourceProperties.getInstance(ResourceProperties.java:52)
at de.mpa.task.Task.(Task.java:67)
at de.mpa.task.instances.SpectraTask.(SpectraTask.java:25)
at de.mpa.cli.CmdLineInterface.call(CmdLineInterface.java:243)
at de.mpa.cli.CmdLineInterface.(CmdLineInterface.java:79)
at de.mpa.cli.CmdLineInterface.main(CmdLineInterface.java:335)
(mpa-portable) curangalt-osx:Biofilm_proteins curanga$