Fix docker args in GLNexusHandler

BimberLab · Feb 1, 2024 · 2407a00 · 2407a00
1 parent db93852
commit 2407a00
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -266,7 +266,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 throw new PipelineJobException(e);
             }
 
-            execute(Arrays.asList(localBashScript.getPath()));
+            execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
 
             if (!outputVcf.exists())
             {

diff --git a/singlecell/resources/views/singleCellDataManagement.html b/singlecell/resources/views/singleCellDataManagement.html
@@ -42,6 +42,9 @@
                     },{
                         name: 'Readsets Assigned to Run Lacking Data',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_readsets', 'query.viewName': 'Assigned to Run Lacking Data'})
+                    },{
+                        name: 'cDNA Libraries with Hashing and Single HTO/Lane',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'singlecell', queryName: 'cdna_libraries', 'query.uniqueHtos~in': '0;1', 'query.hashingReadsetId/name~isnonblank': null, 'query.hashingReadsetId/totalFiles~eq': 0})
                     },{
                         name: 'Analyses In Novogene-Related Workbook',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.container/title~containsoneof': 'Novogene;shipment'})