From 2407a002355ab2948c39836125c04ac6e877dff2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 31 Jan 2024 16:56:49 -0800 Subject: [PATCH] Fix docker args in GLNexusHandler --- .../org/labkey/sequenceanalysis/analysis/GLNexusHandler.java | 2 +- singlecell/resources/views/singleCellDataManagement.html | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java index 8a6620566..d9e323c5f 100644 --- 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 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 index 6be435912..7e4f2835d 100644 --- 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'})