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Add InstaNovo support to DeNovoGUI #53

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Add InstaNovo support to DeNovoGUI #53

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690a116
Add InstaNovo workflows to DeNovoGUI
BioGeek Jun 23, 2026
85d3794
Add InstaNovo job tests
BioGeek Jun 23, 2026
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28 changes: 17 additions & 11 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -325,10 +325,10 @@
<scope>test</scope>
</dependency>

<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>4.12.15</version>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>utilities</artifactId>
<version>5.1.17</version>
<exclusions>
<exclusion>
<artifactId>commons-math</artifactId>
Expand Down Expand Up @@ -370,13 +370,19 @@
<artifactId>ols-dialog</artifactId>
<groupId>no.uib</groupId>
</exclusion>
</exclusions>
<type>jar</type>
</dependency>

<dependency>
<groupId>jfree</groupId>
<artifactId>jfreechart</artifactId>
</exclusions>
<type>jar</type>
</dependency>

<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>2.25.4</version>
</dependency>

<dependency>
<groupId>jfree</groupId>
<artifactId>jfreechart</artifactId>
<version>1.0.13</version>
</dependency>

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16 changes: 0 additions & 16 deletions src/log4j.properties
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4 changes: 2 additions & 2 deletions src/main/java/com/compomics/denovogui/DeNovoGUIWrapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import com.compomics.denovogui.util.Properties;
import com.compomics.software.CompomicsWrapper;
import com.compomics.software.settings.PathKey;
import com.compomics.software.settings.UtilitiesPathPreferences;
import com.compomics.software.settings.UtilitiesPathParameters;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
Expand Down Expand Up @@ -89,7 +89,7 @@ protected String getJarFilePath() {
* Sets the path configuration.
*/
private void setPathConfiguration() throws IOException {
File pathConfigurationFile = new File(getJarFilePath(), UtilitiesPathPreferences.configurationFileName);
File pathConfigurationFile = new File(getJarFilePath(), UtilitiesPathParameters.configurationFileName);
if (pathConfigurationFile.exists()) {
DeNovoGUIPathPreferences.loadPathPreferencesFromFile(pathConfigurationFile);
}
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