Merge pull request #402 from LabKey/fb_merge_25.11_to_develop

Merge 25.11 to develop

Author: bbimber

.github/dependabot.yml

@@ -4,4 +4,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "weekly"

SequenceAnalysis/pipeline_code/extra_tools_install.sh

@@ -350,3 +350,32 @@ then
 else
     echo "Already installed"
 fi
+
+
+echo ""
+echo ""
+echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
+echo "Install hifiasm"
+echo ""
+cd $LKSRC_DIR
+if [[ ! -e ${LKTOOLS_DIR}/primer3_core || ! -z $FORCE_REINSTALL ]];
+then
+    echo "Cleaning up previous installs"
+    rm -Rf $LKTOOLS_DIR/hifiasm*
+    rm -Rf $LKTOOLS_DIR/yak*
+    rm -Rf hifiasm*
+    rm -Rf yak*
+
+    git clone https://github.com/chhylp123/hifiasm
+    cd hifiasm
+    make
+    install hifiasm $LKTOOLS_DIR/
+    cd ../
+
+    git clone https://github.com/lh3/yak
+    cd yak
+    make
+    install yak $LKTOOLS_DIR/
+else
+    echo "Already installed"
+fi

SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml

@@ -20,6 +20,7 @@
        <column name="totalFiles" />
        <column name="readdataWithoutSra" />
        <column name="files" />
+       <column name="continer/title" />
    </columns>
    <sorts>
        <sort column="rowid" descending="true"/>

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java

@@ -14,7 +14,6 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.collections.IntHashMap;
-import org.labkey.api.assay.AssayFileWriter;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.SimpleFilter;

cluster/src/org/labkey/cluster/pipeline/ClusterPipelineJob.java

@@ -169,8 +169,6 @@ public Task<ClusterTaskFactory> createTask(PipelineJob job)
                 @Override
                 public RecordedActionSet run() throws PipelineJobException
                 {
-                    job.setStatus(TaskStatus.running, "I am running!");
-
                     ((ClusterPipelineJob)getJob()).getRunnable().run(getJob().getLogger());
 
                     return new RecordedActionSet();

jbrowse/package-lock.json

@@ -52,6 +52,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -637,20 +638,31 @@ public enum Chemistry
 
         public File getInclusionListFile(Logger logger) throws PipelineJobException
         {
-            File exe = new CellRangerWrapper(logger).getExe();
+            File exe = new CellRangerWrapper(logger).getExe().getAbsoluteFile();
+            logger.debug("cellranger executable: " + exe.getPath());
             if (Files.isSymbolicLink(exe.toPath()))
             {
                 try
                 {
-                    exe = Files.readSymbolicLink(exe.toPath()).toFile();
+                    Path exePath = Files.readSymbolicLink(exe.toPath());
+                    logger.debug("cellranger symlink target: " + exePath);
+                    if (!exePath.isAbsolute())
+                    {
+                        File parent = exe.getParentFile();
+                        exePath = parent.toPath().resolve(exePath);
+                        logger.debug("resolved symlink target: " + exePath);
+                    }
+
+                    exe = exePath.toFile();
+                    logger.debug("cellranger resolved symlink target: " + exe.getPath());
                 }
                 catch (IOException e)
                 {
                     throw new PipelineJobException(e);
                 }
             }
 
-            File il = new File(exe.getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile);
+            File il = new File(exe.getParentFile(), "../lib/python/cellranger/barcodes/" + _inclusionListFile);
             if (!il.exists())
             {
                 throw new PipelineJobException("Unable to find file: " + il.getPath());